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Sample GSM824869 Query DataSets for GSM824869
Status Public on Nov 01, 2011
Title SK-N-MC-DS14413
Sample type RNA
 
Source name Neuroepithelioma cell line derived from a metastatic supra-orbital human brain tumor
Organism Homo sapiens
Characteristics biomaterial_type: immortalized cell line
lab: UW
lab description: Stamatoyannopoulous - University of Washington
datatype: AffyExonArray
datatype description: Affymetrix Exon Microarray
line: SK-N-MC
cell organism: human
cell description: neuroepithelioma cell line derived from a metastatic supra-orbital human brain tumor, "SK-N-MC was isolated in September of l971 and was found to have moderate dopamine - beta - hydroxylase activity as well as formaldehyde induced fluorescence indicative of intracellular catecholamines." - ATCC. (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.)
cell karyotype: cancer
cell lineage: ectoderm
cell sex: F
labexpid: RS17574
replicate: 2
Biomaterial provider ATCC;HTB-10
Growth protocol Followed vendor recommendations for growth protocol/media
Extracted molecule total RNA
Extraction protocol At cell harvest, a subset of cells was stored at -20oC in RNALater. Total RNA from 5 X 10^6 cells were purified using Ribopure (Ambion) according to vendor recommended protocols. Total RNA quality was assessed on RNA 6000 Nano Chips (Agilent) using a Bioanalyzer (Agilent).
Label biotin
Label protocol A Whole Transcript Sense Target Labeling Assay (Affymetrix) was used to reduce the rRNA, perform in vitro transcription (IVT) and create labeled sense strand DNA for hybridization to the arrays.
 
Hybridization protocol Hybridizations were carried out according the manufacturer (Affymetrix) protocol
Scan protocol Affymterix Gene Chip Scanner 3000
Description http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeUwAffyExonArray
Data processing Intensity files from the scanned exon arrays were analyzed at the exon level (Affymetrix ExACT 1.2.1 software). Sample data were quantile normalized with PM-GCBG background correction and PLIER (Probe Logarithmic Intensity Error) summarized
HuEx-1_0-st-v2.r2.pgf
quantile normalized with PM-GCBG background correction and PLIER (Probe Logarithmic Intensity Error) summarized
 
Submission date Oct 31, 2011
Last update date Jul 29, 2016
Contact name ENCODE DCC
E-mail(s) encode-help@lists.stanford.edu
Organization name ENCODE DCC
Street address 300 Pasteur Dr
City Stanford
State/province CA
ZIP/Postal code 94305-5120
Country USA
 
Platform ID GPL5188
Series (1)
GSE19090 Exon arrays of ENCODE tier 1, tier 2 and tier 3 cell types

Data table header descriptions
ID_REF
VALUE quantile normalized with PM-GCBG background correction and PLIER (Probe Logarithmic Intensity Error) summarized

Data table
ID_REF VALUE
2315101 103.7253
2315102 117.7295
2315104 138.7193
2315105 54.22667
2315107 269.4589
2315112 69.10263
2315114 136.4539
2315116 138.2377
2315118 1130.357
2315120 454.5952
2315126 15.25973
2315132 0.0001758516
2315138 131.3002
2315140 44.54861
2315142 12.74252
2315144 12.14124
2315146 75.5581
2315148 112.6266
2315149 275.7582
2315150 123.2168

Total number of rows: 1384231

Table truncated, full table size 22705 Kbytes.




Supplementary file Size Download File type/resource
GSM824869_X_Hs_SKNMC_E_101230_10_RS17574_W.CEL.gz 24.2 Mb (ftp)(http) CEL
GSM824869_hg19_wgEncodeUwAffyExonArraySknmcSimpleSignalRep2.broadPeak.gz 21.1 Mb (ftp)(http) BROADPEAK
Raw data provided as supplementary file
Processed data included within Sample table
Processed data provided as supplementary file

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