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Sample GSM1001392 Query DataSets for GSM1001392
Status Public on Oct 25, 2012
Title high-Myc - Replicate 2
Sample type RNA
 
Source name P493-6 cells expressing a high level of c-Myc
Organism Homo sapiens
Characteristics cell line: P493-6
cell type: B-cell lymphoma
Treatment protocol c-Myc expression released for 24 hours.
Growth protocol RPMI 1640 + FBS. Tetracycline repressed c-Myc transgene expression. c-Myc expression released for 24 hours.
Extracted molecule total RNA
Extraction protocol Trizol extraction of total RNA was performed according to the manufacturer's instructions.
External spike-in RNAs (ERCC ExFold RNA Spike-In kit, Ambion, 4456739) were added based on cell number. See manuscript for details.
Label biotin
Label protocol Biotinylated aRNA was prepared according to the standard Affymetrix protocol from 100 ng total RNA (GeneChip 3' IVT Express Kit User Manual, 2009, Affymetrix).
 
Hybridization protocol Following fragmentation, 12.5 ug of aRNA were hybridized at 45C for 16 hr at 60RPM on GeneChip Arrays (PrimeView). GeneChips were washed and stained in the Affymetrix Fluidics Station 450 according to the manurfacturer's instructions, using the buffers provided in the Affymetrix GeneChip Hybridization, Wash and Stain Kit.
Scan protocol GeneChips were scanned using the GeneChip Scanner 3000 and images were extracted with Affymetrix GeneChip Expression Console. A CDF containing the ERCC probes was provided by Affymetrix.
Data processing A CDF provided by Affymetrix, which contained the ERCC probes (PrimeView_withERCC_binary.cdf) was used instead of the standard PrimeView cdf.
The data were analyzed with Bioconductor using the MAS5 normalization method. Then, these data were renormalized to the external spike-ins. See manuscript for additional details.
 
Submission date Sep 11, 2012
Last update date May 19, 2015
Contact name Richard A Young
E-mail(s) young_computation@wi.mit.edu
Phone 617-258-5219
Organization name Whitehead Institute for Biomedical Research
Lab Young Lab
Street address 9 Cambridge Center
City Cambridge
State/province MA
ZIP/Postal code 02142
Country USA
 
Platform ID GPL16043
Series (2)
GSE40782 Revisiting Global Gene Expression Analysis (Microarray)
GSE40784 Revisiting Global Gene Expression Analysis

Data table header descriptions
ID_REF
VALUE MAS 5.0 signal intensity
renorm_GSM1001392

Data table
ID_REF VALUE renorm_GSM1001392
11715100_at 25.82582415 32.91016668
11715101_s_at 56.9260735 84.10910518
11715102_x_at 32.34093075 42.38211344
11715103_x_at 74.74141416 115.8746518
11715104_s_at 28.11309388 36.90544461
11715105_at 11.10219209 12.22496198
11715106_x_at 30.18896363 38.78050831
11715107_s_at 29.5418889 38.53595289
11715108_x_at 12.64476111 13.90492966
11715109_at 21.7432324 26.50230311
11715110_at 42.14321165 59.05521403
11715111_s_at 134.7948505 216.04215
11715112_at 11.60641801 12.79452441
11715113_x_at 119.8896092 188.4387527
11715114_x_at 153.3502836 241.9564678
11715115_s_at 9.386764868 9.916219824
11715116_s_at 31.9371497 41.97049735
11715117_x_at 21.34191746 25.38976115
11715118_s_at 13.99526617 16.22572937
11715119_s_at 13.99317283 15.90908993

Total number of rows: 49495

Table truncated, full table size 1803 Kbytes.




Supplementary file Size Download File type/resource
GSM1001392_3B_PrimeView_.CEL.gz 1.9 Mb (ftp)(http) CEL
Processed data included within Sample table

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