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Sample GSM750894 Query DataSets for GSM750894
Status Public on Jun 30, 2011
Title sh-JMJD1B_rep2
Sample type RNA
 
Source name sh-JMJD1B
Organism Homo sapiens
Characteristics cell line: K562
genotype/variation: JMJD1B knock-down
Treatment protocol Stable cells were treated 1 ug/ml doxyclcline for 48 h.
Growth protocol K562 cells in RPMI1640 medium supplemented with 5 % fetal bovine serum (FBS) and 0.05 % antibiotics at 37 C in a 5 % CO2 atmosphere
Extracted molecule total RNA
Extraction protocol RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.
Label biotin
Label protocol Biotinylated cRNA were prepared from 0.55 ug total RNA using the Illumina TotalPrep RNA Amplification Kit (Ambion, Austin,TX).
 
Hybridization protocol Following fragmentation, 0.75 ug of cRNA were hybridized to the Illumina HumanHT-12 Expression Beadchip according to the protocols provided by the manufacturer.
Scan protocol Arrays were scanned using the Illumina Bead Array ReaderĀ  Confocal Scanner
Description Tet-on system
Data processing Array data export processing and analysis was performed using Illumina GenomeStudio v2009.2 Gene Expression Module v1.5.4.Array data were filtered by detection p-value < 0.05 (similar to signal to noise) and the selected probe signal values were transformed by logarithm and normalized by quantile method.
 
Submission date Jun 29, 2011
Last update date May 17, 2012
Contact name jiyoung kim
E-mail(s) gene5486@hanmail.net
Organization name Chung-Ang University
Street address Heusokdong
City seoul
ZIP/Postal code 156-756
Country South Korea
 
Platform ID GPL10558
Series (1)
GSE30294 JMJD1B target gene screening :JMJD1B is the H3K9 demethylase involved in transcriptional activation of Lmo2 in leukemia

Data table header descriptions
ID_REF
VALUE quantile normalized
Detection Pval

Data table
ID_REF VALUE Detection Pval
ILMN_1901419 4148.47 0
ILMN_1716859 759.686 0
ILMN_1699723 3915.155 0
ILMN_1801442 349.1299 0
ILMN_1846306 269.9956 0
ILMN_2171289 375.8593 0
ILMN_1800276 268.8269 0
ILMN_1811303 896.8633 0
ILMN_2096372 1522.046 0
ILMN_1753663 262.1685 0
ILMN_1688335 648.809 0
ILMN_1662843 249.175 0
ILMN_1663916 633.6703 0
ILMN_2351298 272.2137 0
ILMN_1677723 909.2905 0
ILMN_1652975 1312.896 0
ILMN_2086890 1445.921 0
ILMN_1763452 399.9057 0
ILMN_3243112 646.6937 0
ILMN_1740633 409.9816 0

Total number of rows: 19144

Table truncated, full table size 482 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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