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Sample GSM1535134 Query DataSets for GSM1535134
Status Public on Dec 01, 2014
Title Normal_Prostate_HSPH0127
Sample type RNA
 
Source name FFPE normal prostate
Organism Homo sapiens
Characteristics rs13385191: 0
rs1465618: 1
rs721048: 2
rs12621278: 2
rs2292884: 0
rs2660753: 0
rs7629490: NA
rs17021918: 1
rs7679673: 1
rs12653946: 0
rs1983891: NA
rs339331: 1
rs9364554: 0
rs12155172: 1
rs10486567: 2
rs6465657: 0
rs2928679: 2
rs1512268: 2
rs1016343: 1
rs16901979: 0
rs16902094: 0
rs620861: 1
rs6983267: 1
rs4242382: NA
rs1571801: 0
rs10993994: 0
rs7127900: 0
rs12418451: 0
rs10896449: 1
rs902774: 0
rs11649743: 2
rs4430796: 1
rs1859962: 1
rs8102476: 0
rs11672691: 2
rs2735839: 2
rs5759167: 1
rs11704416: 1
rs5945619: 0
Extracted molecule total RNA
Extraction protocol Not provided
Label biotin
Label protocol Not provided
 
Hybridization protocol Not provided
Scan protocol Not provided
Data processing For the expression profiles generated, we regressed out technical variables including mRNA concentration, age of the block, batch (96-well plate), percent of the probes on the array detectable above the background, log transformed average background signal, and the median of the perfect match probes for each probe intensity of the raw data. The residuals were then shifted to have the original mean expression values and normalized using the RMA method. We mapped gene names to Affymetrix transcript cluster IDs using the NetAffx annotations as implemented in Bioconductor annotation package pd.hugene.1.0.st.v1; this resulted in 20,254 unique named genes. As gene names were used in the final analysis, this is what we have included in the sample tables.
 
Submission date Oct 30, 2014
Last update date Dec 01, 2014
Contact name Kathryn Penney
Organization name Brigham and Women's Hospital
Department Medicine
Lab Channing Division of Network Medicine
Street address 181 Longwood Ave
City Boston
ZIP/Postal code 02115
Country USA
 
Platform ID GPL19370
Series (1)
GSE62872 Association of Prostate Cancer Risk Variants with Gene Expression in Normal and Tumor Tissue

Data table header descriptions
ID_REF
VALUE Normalized expression values linked to gene names using the details provided in the 'data processing' section

Data table
ID_REF VALUE
OR4F17 1.618836
OR4F16 3.289762
LOC643837 3.693518
SAMD11 4.228088
KLHL17 4.078391
PLEKHN1 4.509011
ISG15 3.618341
AGRN 3.768331
MIR200B 3.145822
MIR200A 1.663031
MIR429 2.868781
TTLL10 4.332981
B3GALT6 4.159353
SCNN1D 4.548735
PUSL1 4.492466
TAS1R3 3.505154
VWA1 4.640434
ATAD3C 3.025191
ATAD3A 4.294295
ATAD3B 3.853799

Total number of rows: 20254

Table truncated, full table size 309 Kbytes.




Supplementary file Size Download File type/resource
GSM1535134_265.CEL.gz 3.6 Mb (ftp)(http) CEL
Processed data included within Sample table

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