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Sample GSM569500 Query DataSets for GSM569500
Status Public on Jul 24, 2010
Title GM17103
Sample type RNA
 
Source name Lymphoblastoid cell line GM17103
Organism Homo sapiens
Characteristics ethnic group: AA African-American
cell line (coriell id): GM17103
wei id: Wei015
cell type: EBV-transformed lymphoblastoid cells
Biomaterial provider Coriell Cell Repositories http://ccr.coriell.org/Sections/Search/Search.aspx?PgId=165&q=GM17103
Treatment protocol No treatment was used.
Growth protocol LCLs were cultured in RPMI 1640 medium supplemented with 15% heat-inactivated Fetal Bovine Serum (FBS). According to the protocol from the Coriell website (http://ccr.coriell.org/sections/support/global/lymphoblastoid.aspx?pgid=213), LCLs were maintained at a density of 2-8 × 10^5 cells/ml, and were split or re-fed with fresh medium every three days, depending on the growth status of each cell line.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from each of the cell lines using Qiagen RNeasy Mini kits (QIAGEN, Inc.). RNA quality was tested using an Agilent 2100 Bioanalyzer.
Label biotin
Label protocol Labeling was performed according to the Affymetrix Gene Chip technical manual.
 
Hybridization protocol The targets for Affymetrix DNA microarray analysis were prepared according to the manufacturer’s instructions. Biotin-labeled cRNA, produced by in vitro transcription, was fragmented and hybridized to Affymetrix GeneChip Human Genome U133 Plus 2.0 Arrays at 45°C for 16 hr and then washed and stained using the GeneChip Fluidics.
Scan protocol The arrays were scanned by a GeneArray Scanner and patterns of hybridization detected as light emitted from the fluorescent reporter groups incorporated into the target and hybridized to oligonucleotide probes.
Description Basal gene expression level of lymphoblastoid cell line GM17103.
Data processing The data were analyzed with Agilent Gene Spring GX 7.3 version using Affymetrix default analysis settings and GC-RMA as the normalization method.
 
Submission date Jul 23, 2010
Last update date Sep 24, 2010
Contact name Liewei Wang
E-mail(s) wang.liewei@mayo.edu
Phone 507-284-5264
Fax 507-284-4455
URL http://mayoresearch.mayo.edu/staff/wang_l2.cfm
Organization name Mayo Clinic
Department Molecular Pharmacology and Experimental Therapeutics
Street address 200 First street SW
City Rochester
State/province MN
ZIP/Postal code 55905
Country USA
 
Platform ID GPL570
Series (2)
GSE23120 Basal gene expression data from Human Variation Panel
GSE24277 Human Variation Panel: Gene Expression and Genotype

Data table header descriptions
ID_REF
VALUE GCRMA normalized signal intensity

Data table
ID_REF VALUE
1007_s_at 54.51
1053_at 510.4
117_at 32.62
121_at 65.44
1255_g_at 4.997
1294_at 263.4
1316_at 7.239
1320_at 5.506
1405_i_at 181
1431_at 7.017
1438_at 6.065
1487_at 187.6
1494_f_at 6.693
1552256_a_at 966.6
1552257_a_at 548.7
1552258_at 7.782
1552261_at 7.214
1552263_at 195.1
1552264_a_at 465.6
1552266_at 8.349

Total number of rows: 54613

Table truncated, full table size 887 Kbytes.




Supplementary file Size Download File type/resource
GSM569500.cel.gz 4.6 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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