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Sample GSM531865 Query DataSets for GSM531865
Status Public on Feb 28, 2012
Title 5_23dox-
Sample type RNA
 
Source name NT2D1 cell line, total RNA
Organism Homo sapiens
Characteristics cell type: embryonal carcinoma cell line
cell line: NT2D1
genotype/variation: stably expressing TetR3 and L1TD1shRNA
dox treatment: dox-
time point: Day 6
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using RNeasy Kit (Qiagen). To eliminate genomic DNA DNase I (Qiagen) digestion in column was included. RNA/cRNA concentrations where checked with Nanodrop ND-1000 and RNA/cRNA quality was controlled by BioRad’s Experion electrophoresis station
Label biotin
Label protocol Ambion's Illumina RNA TotalPrep Amplification kit (cat no AMIL1791)
 
Hybridization protocol Standard Illumina hybridization protocol
Scan protocol Standard Illumina scanning protocol
Description replicate 4
Data processing The data was analyzed with R language and environment for statistical computing (version 2.10.1) using the Bioconductor module (version 2.5), quantile normalization method from limma package was used. Limma package computed normalized signal intensities.
 
Submission date Apr 09, 2010
Last update date Feb 28, 2012
Contact name Nelly Rahkonen
E-mail(s) nelly.rahkonen@btk.fi
Organization name Turku Centr for Biotechnology
Street address Tykistökatu 6 A
City Turku
ZIP/Postal code 20520
Country Finland
 
Platform ID GPL6947
Series (1)
GSE21275 Genome wide analysis of long term L1TD1 knockdown effects in NT2D1 cell line with inducible shRNA vectors

Data table header descriptions
ID_REF
VALUE quantile normalized
Detection Pval

Data table
ID_REF VALUE Detection Pval
ILMN_1802380 1343.516 0
ILMN_1893287 64.43077545 0.8985507
ILMN_1736104 75.45062091 0.3873518
ILMN_1792389 587.1911182 0
ILMN_1854015 107.2136973 0.01581028
ILMN_1904757 178.4064909 0
ILMN_1740305 72.79619818 0.5125165
ILMN_1665168 63.86436364 0.9117259
ILMN_2375156 79.62813455 0.2108037
ILMN_1705423 74.86179091 0.4163373
ILMN_1716072 67.20567136 0.8076416
ILMN_1697642 216.7967727 0
ILMN_1788184 85.83418091 0.09486166
ILMN_1681845 449.6309818 0
ILMN_1823296 65.76731182 0.8524374
ILMN_1889845 75.67195182 0.3781291
ILMN_1746923 78.50708364 0.2397892
ILMN_1690979 110.9230455 0.01449275
ILMN_1811114 76.77194273 0.3267457
ILMN_1660729 76.44256545 0.3372859

Total number of rows: 48803

Table truncated, full table size 1575 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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