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Sample GSM421933 Query DataSets for GSM421933
Status Public on Dec 10, 2009
Title U937 cells with knock-down of Pirin - Replica 1
Sample type RNA
 
Source name U937 myelomonocytic cell line, PIR knock-down
Organism Homo sapiens
Characteristics cell line: U937
pir knock-down: yes
Growth protocol U937 cell lines were maintained in RPMI-1640 supplemented with 10% FCS and 2mM glutamine at 37°C in a humidified atmosphere containing 5% CO2.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using TRIzol Reagent (Gibco), followed by clean up on RNeasy mini/midi columns (RNeasy Mini/Midi Kit, Qiagen). For each sample, an RNA pool was obtained by mixing equal quantities of total RNA from each of the three independent RNA extractions.
Label biotin
Label protocol Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA The size and the accuracy of quantitation of targets were checked by agarose gel electrophoresis of 2ug aliquots, prior to and after fragmentation. After fragmentation, targets were diluted in hybridisation buffer at a concentration of 150ug/ml.
 
Hybridization protocol Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip GeneChip HG-U133 Plus v.2 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station. Two copies of the GeneChip HG-U133 Plus v.2 were hybridized with each biotin-labeled target.
Scan protocol Images were scanned using an Affymetrix GeneArray Scanner, using default parameters.
Description U937 is a human cell line established from a diffuse histiocytic lymphoma and displaying monocytic characteristics.
Data processing The data were analyzed with GeneChip operating system (GCOS) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.
 
Submission date Jun 24, 2009
Last update date Aug 28, 2018
Contact name Myriam Alcalay
E-mail(s) myriam.alcalay@ieo.eu
Organization name European Institute of Oncology
Department Experimental Oncology
Lab Functional Genomics
Street address Via Adamello 16
City Milan
ZIP/Postal code 20139
Country Italy
 
Platform ID GPL570
Series (1)
GSE16798 Genes regulated after knock-down of Pirin in U937 cells
Relations
Reanalyzed by GSE119087

Data table header descriptions
ID_REF
VALUE GCOS signal intensity
ABS_CALL the call in an absolute analysis that indicates if 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
1007_s_at 42.1 A 0.458816
1053_at 2688.1 P 0.000219
117_at 167.9 P 0.000388
121_at 464.4 P 0.011447
1255_g_at 20.5 A 0.602006
1294_at 599.2 P 0.000388
1316_at 78.6 P 0.035163
1320_at 17.5 A 0.781017
1405_i_at 6561.4 P 0.000491
1431_at 97.7 P 0.007543
1438_at 12.8 A 0.837065
1487_at 1130.2 P 0.009985
1494_f_at 100.4 P 0.017001
1552256_a_at 4452.1 P 0.000244
1552257_a_at 1703.2 P 0.000732
1552258_at 72.2 A 0.27417
1552261_at 32.6 A 0.366211
1552263_at 504.2 P 0.000244
1552264_a_at 1236.6 P 0.000244
1552266_at 37 A 0.111572

Total number of rows: 54675

Table truncated, full table size 1432 Kbytes.




Supplementary file Size Download File type/resource
GSM421933.CEL.gz 4.8 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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