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Sample GSM1103977 Query DataSets for GSM1103977
Status Public on Oct 01, 2013
Title Vehicle treated, no doxycycline; biological replicate 2
Sample type RNA
 
Source name U937-derived cell line harboring TRIPZ-shRNAmir TetOn cassette (clone ID: V3THS-381738)
Organism Homo sapiens
Characteristics cell line: U937
cell type: histiocytic lymphoma
genotype/variation: control
agent: vehicle
Treatment protocol Individual cell lines were treated with 0.5 ug/mL doxycycline every day for four days to achieve inducible knockdown of ZXDC1/2. After the first two days of doxycycline treatment, cell lines were treated with either 100 nM PMA or vehicle (0.1% DMSO) and allowed to differentiate for 3 days.
Growth protocol U937 stably transduced with TRIPZ-shRNAmir (Thermo/OpenBiosystems) were cultured in RPMI + 10% FBS, 100 U/mL penicilli, 100 ug/mL streptomycin, and 0.5 ug/mL Puromycin
Extracted molecule total RNA
Extraction protocol Total RNA was extracted via Qiagen Rneasy Micro kit according to the manufacturer's instruction
Label biotin
Label protocol Biotinylated cRNA were prepared according to the GeneChip 3' IVT Express kit from 100 ng total RNA (Affymetrix catolog # 901228).
 
Hybridization protocol Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array in a GeneChip hybridization oven 640. GeneChips were singly scanned using a Genechip scanner 3000 7G with autoloader. Fluidics and scan functions were controlled by Command Console software ver 1.1 (AGCC).
Scan protocol GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
Description Veh_Veh_2
Gene expression data from cell line treated with vehicle in the absence of doxycycline-inducible knockdown of ZXDC1/2
Data processing The data were analyzed with AltAnalyze version 2.02 beta, using RMA for normalization.
 
Submission date Mar 22, 2013
Last update date Oct 01, 2013
Contact name Joseph Fontes
E-mail(s) [email protected]
Organization name Univ Kansas Medical Center
Department Biochemistry and Molecular Biology
Street address 3901 Rainbow Blvd
City Kansas City
State/province KS
ZIP/Postal code 66160
Country USA
 
Platform ID GPL570
Series (1)
GSE45417 Expression data from knockdown of ZXDC1/2 in PMA-treated U937

Data table header descriptions
ID_REF
VALUE log2-GC-RMA signal

Data table
ID_REF VALUE
1007_s_at 5.23362
1053_at 9.50027
117_at 5.85804
121_at 7.34242
1255_g_at 2.5711
1294_at 6.20858
1316_at 6.68946
1320_at 3.51342
1405_i_at 10.5847
1431_at 4.15186
1438_at 5.62301
1487_at 8.0261
1494_f_at 5.69676
1552256_a_at 8.49454
1552257_a_at 8.11386
1552258_at 5.40902
1552261_at 4.01824
1552263_at 8.57633
1552264_a_at 8.5043
1552266_at 2.5558

Total number of rows: 54675

Table truncated, full table size 1001 Kbytes.




Supplementary file Size Download File type/resource
GSM1103977_VEH_VEH2.CEL.gz 4.8 Mb (ftp)(http) CEL
Processed data included within Sample table

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