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Sample GSM428011 Query DataSets for GSM428011
Status Public on Jan 01, 2010
Title Total_48h-9b
Sample type RNA
 
Source name P493-6 B cells
Organism Homo sapiens
Characteristics time point: 48 hours
replicate: 9
Treatment protocol P493-6 cells were grown in the presence or absence of tetracycline for the time periods indicated, ectopic Myc gene expression is repressed in the presence of tetracycline and induced following its removal.
Growth protocol P493-6 cells were grown in RPMI Medium 1640 supplemented with 10% heat-inactivated fetal bovine serum, MEM non-essential amino acids, and antibiotic-antimycotic, in a humidified incubator (95% air and 5% CO2) at 37⁰C.
Extracted molecule total RNA
Extraction protocol Nuclear run-on RNA (following in vitro labeling) was purified using a modified Qiagen RNeasy RNA Isolation procedure. Total RNA was extracted with Trizol reagent, followed by clean-up 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 Nuclear run-on RNA was labeled by first adding biotin-modified UTP to isolated nuclei for 30 mins. Biotinylated nuclear run-on RNA was captured on avidin magnetic beads followed by first strand synthesis (directly on beads) and second strand synthesis (in solution). Biotinylated cRNA was supsequently prepared using the Ambion TotalPrep RNA Amplification Kit. Total RNA was labled with the Ambion TotalPrep RNA Amplification Kit according to manufacturers suggested protocols.
 
Hybridization protocol Standard Illumina hybridization protocol
Scan protocol Standard Illumina scanning protocol
Description Total_48h-9b
Data processing The data were normalised using z transformation
 
Submission date Jul 15, 2009
Last update date Jul 15, 2009
Contact name chris cheadle
E-mail(s) ccheadl1@jhmi.edu
Phone 4105505984
Organization name JHU
Department SOM
Lab JHBMC Genomics Core
Street address 5200 Eastern Ave
City baltimore
State/province MD
ZIP/Postal code 21224
Country USA
 
Platform ID GPL6255
Series (1)
GSE17109 MYC Transactome Mapped by Global Array-based Nuclear Run-on (ANRO)

Data table header descriptions
ID_REF
VALUE z score

Data table
ID_REF VALUE
ILMN_10000 0.30653012
ILMN_10001 1.6309942
ILMN_10002 -0.9301356
ILMN_10004 0.67831895
ILMN_10005 1.54671075
ILMN_10006 -0.5734864
ILMN_10009 -0.384266
ILMN_1001 -0.7986368
ILMN_10010 -0.7419298
ILMN_10011 0.25279693
ILMN_10012 -0.7955451
ILMN_10013 -0.7652963
ILMN_10014 -0.6186508
ILMN_10016 -0.5945482
ILMN_1002 -0.8889573
ILMN_10020 -0.6247969
ILMN_10021 0.34951589
ILMN_10022 -0.7150781
ILMN_10023 -0.9563306
ILMN_10024 -0.6837858

Total number of rows: 20589

Table truncated, full table size 434 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
Processed data are available on Series record

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