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Sample GSM1178276 Query DataSets for GSM1178276
Status Public on Jul 01, 2013
Title K-562_originating cell line_R3
Sample type RNA
 
Source name K-562, originating cell line
Organism Homo sapiens
Characteristics originating cell line: K-562
tumor type: chronic myelogenous (blast crisis) leukemia
in vivo passage: P0
Treatment protocol N/A
Growth protocol All cell lines were obtained from the Division of Cancer Treatment and Diagnosis Tumor Repository (DTP, FNLCR, Frederick, MD) or American Type Culture Collection (ATCC) (Manassas, Va). In addition, the identities of all cell lines used in this study were confirmed using Identifiler® STR genotyping (Applied Biosystems). All mice used in the study were obtained from the Animal Production Program (FNLCR, Frederick, MD). Tumor cells for inoculation were derived from the 4th in vitro passage from cryopreserved cell stocks. Cells (1 x 10^7 cells/0.1 ml/inoculation) were inoculated subcutaneously into mice (n=10 or more mice depending on the tumor cell line). For comparative purposes, 2-3 samples of in vitro cultivated cells at passage 4 post-cryopreservation were also prepared for microarray analysis (P0). When tumors at P1, P4 and P10 reached approximately 500 mg (10x10 mm), 5 tumors were harvested, cut into small pieces and flash frozen in liquid nitrogen using pre-chilled tubes. Samples were transferred to a -70°C freezer for holding prior to processing. Serial tumor passage was achieved by harvesting donor tumor material (n=2 to 5 donors) at each passage, mincing the tumors (2x2 mm fragments), pooling the samples and inoculating the next recipients subcutaneously using tumor implant trocars. Athymic nude mice (nu/nu NCr) served as the primary host for most xenograft studies. In several instances (particularly with human leukemias and lymphomas) it was difficult to establish and passage tumors in nu/nu NCr mice. In these instances, SCID.NCr or NOD.SCID/NCr mice were assessed for suitability. In general, female mice were used as they are less aggressive, easily group-housed and routinely used in xenograft experiments. Male mice were used for prostate tumors (PC-3, PC-3/M). Finally, in those instances where hormone effects on tumor growth are important (e.g., estradiol-dependent breast), mice were supplemented with estradiol.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated using RNeasy (Qiagen).
Label Biotin
Label protocol The RNA samples were submitted to Expression Analysis, Inc. (Durham, NC) for microarray analysis using the GeneChip® Human U133 Plus 2.0 Array (Affymetrix, Santa Clara, CA). Samples were labeled according to the "Affymetrix Technical Manual" (www.expressionanalysis.com).
 
Hybridization protocol Samples were hybridized according to the "Affymetrix Technical Manual" (www.expressionanalysis.com).
Scan protocol Microarray images were captured using a GeneChip® 3000 Scanner.
Description K-562 P0 T3
Gene expression data from K-562 originating cell line.
Data processing Affymetrix Expression Console v1.3.
 
Submission date Jun 30, 2013
Last update date Jul 01, 2013
Contact name Luke Hunter Stockwin
E-mail(s) stockwinl@mail.nih.gov
Phone 301-846-5431
Organization name NCI Frederick
Department DTP
Street address Ft. Detrick
City Frederick
State/province MD
ZIP/Postal code 21701
Country USA
 
Platform ID GPL570
Series (1)
GSE48433 Microarray analysis of xenograft models in use at the Developmental Therapeutics Program of the National Cancer Institute (DTP-NCI)

Data table header descriptions
ID_REF
VALUE MAS5.0 signal intensity
ABS_CALL indicating whether the transcript was present (P), absent (A), or marginal (M)
DETECTION P-VALUE p-value that indicates the significance level of the detection call

Data table
ID_REF VALUE ABS_CALL DETECTION P-VALUE
AFFX-BioB-5_at 712.369 P 0.000662269
AFFX-BioB-M_at 923.755 P 5.16732e-05
AFFX-BioB-3_at 736.814 P 0.00010954
AFFX-BioC-5_at 1645.07 P 9.4506e-05
AFFX-BioC-3_at 2466.6 P 4.42873e-05
AFFX-BioDn-5_at 4880.21 P 4.42873e-05
AFFX-BioDn-3_at 9185.45 P 0.000126798
AFFX-CreX-5_at 23247.2 P 5.16732e-05
AFFX-CreX-3_at 22758.6 P 4.42873e-05
AFFX-DapX-5_at 33.2949 A 0.227636
AFFX-DapX-M_at 29.0534 A 0.39692
AFFX-DapX-3_at 7.68287 A 0.749204
AFFX-LysX-5_at 8.01891 A 0.60308
AFFX-LysX-M_at 9.02713 A 0.772364
AFFX-LysX-3_at 9.56415 A 0.382599
AFFX-PheX-5_at 6.80469 A 0.783476
AFFX-PheX-M_at 65.3659 A 0.262827
AFFX-PheX-3_at 6.514 A 0.672921
AFFX-ThrX-5_at 31.6897 A 0.327079
AFFX-ThrX-M_at 33.7113 A 0.0726999

Total number of rows: 54675

Table truncated, full table size 1628 Kbytes.




Supplementary file Size Download File type/resource
GSM1178276_EA06017_129741_H133+_126.CEL.gz 4.6 Mb (ftp)(http) CEL
GSM1178276_EA06017_129741_H133+_126.CHP.gz 491.5 Kb (ftp)(http) CHP
Raw data provided as supplementary file
Processed data included within Sample table
Processed data provided as supplementary file

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