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Sample GSM427938 Query DataSets for GSM427938
Status Public on Jan 01, 2010
Title NRO_ 1h-8
Sample type other
 
Source name P493-6 B cells
Organism Homo sapiens
Characteristics time point: one hour
replicate: 4
sample: nuclear run-on RNA
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 other
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 NRO_ 1h-8
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 0.13606146
ILMN_10001 -0.6660582
ILMN_10002 -1.1947437
ILMN_10004 0.44503736
ILMN_10005 0.17507288
ILMN_10006 -0.7214384
ILMN_10009 0.13283599
ILMN_1001 -1.0130444
ILMN_10010 -1.0867472
ILMN_10011 1.78631319
ILMN_10012 -1.0637809
ILMN_10013 -0.7798002
ILMN_10014 -0.4880415
ILMN_10016 0.96130031
ILMN_1002 -0.7649127
ILMN_10020 -0.8362066
ILMN_10021 0.27964045
ILMN_10022 -0.9705176
ILMN_10023 -1.041291
ILMN_10024 -0.1895552

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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