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Sample GSM559665 Query DataSets for GSM559665
Status Public on Jul 24, 2010
Title L-UHO-1 siGATA-3 rep3
Sample type RNA
 
Source name siGATA-3 UHO-1
Organism Homo sapiens
Characteristics cell line: UHO-1
sirna: siGATA-3
Treatment protocol U-HO1 and L-1236 cells were transduced with shRNAs against GATA-3 or non-functional control shRNAs, cultured for three days, and sorted according to their GFP positivity.
Growth protocol Cell lines were purchased from DSMZ (Braunschweig, Germany) and cultured in RPMI 1640 supplemented with 10% fetal calf serum (Biochrom; Berlin, Germany), 2 mM glutamine (Invitrogen; Groningen, The Netherlands) and 1% penicillin G/streptomycin sulfate (Invitrogen).UHO-1 cells were cultured as above but in IMDM.
Extracted molecule total RNA
Extraction protocol RNA from 25,000 GFP-positive cells was extracted using the RNeasy Micro Kit (Qiagen, Hilden, Germany). RNA was amplified with the WT expression Kit (Ambion, Austin, USA)
Label biotin
Label protocol Samples were labelled with WT target labelling Kit (Affymetrix, Fremont, USA), washed and stained using the HWS Kit (Affymetrix).
 
Hybridization protocol Human Gene 1.0 ST arrays (Affymetrix) were hybridized with 5.5 mg labelled cDNA.
Scan protocol Affymetrix Gene ChIP Scanner 3000 7G
Description 25,000 GFP-positive cells
Data processing Statistical analysis was done with the statistical computing environment R (version 2.8.1). Additional software packages (affy_1.20.2, vsn_3.8.0, geneplotter_1.20.0, multtest_1.23.3) were taken from the Bioconductor project. Microarray preprocessing: Probe level normalization was conducted using the variance stabilization method (vsn) from Huber et al..
probe group file: Unsupported Human Gene 1.0 ST Array CDF Files
meta-probeset file: HuGene-1_0-st-v1 Probeset Annotations, CSV Format, Release 30 (11 MB 01/22/10)
 
Submission date Jun 24, 2010
Last update date Jun 25, 2010
Contact name Claudia Döring
E-mail(s) C.Doering@em.uni-frankfurt.de
Organization name Johann Wolfgang-Goethe University Frankfurt a.M.
Department Medical School, Institite of Pathology
Street address Theodor Stern Kai 7
City Frankfurt
ZIP/Postal code 60590
Country Germany
 
Platform ID GPL6244
Series (1)
GSE22550 Expression data from Hodgkin lymphoma cell lines UHO-1 and L-1236 transduced with shRNAs against GATA-3 or non-functional control shRNAs

Data table header descriptions
ID_REF
VALUE log2 vsn normalized gene level expression values from Bioconductor

Data table
ID_REF VALUE
7892501 6.139576335
7892502 6.557361841
7892503 5.312074142
7892504 9.600905963
7892505 5.623564245
7892506 6.610030204
7892507 7.429623428
7892508 7.858997689
7892509 12.15003606
7892510 6.209612811
7892511 5.642134239
7892512 7.651916069
7892513 6.068461557
7892514 11.55735268
7892515 9.934878327
7892516 6.771923077
7892517 6.767342595
7892518 5.615565589
7892519 7.096453171
7892520 9.885258774

Total number of rows: 32321

Table truncated, full table size 627 Kbytes.




Supplementary file Size Download File type/resource
GSM559665.CEL.gz 4.4 Mb (ftp)(http) CEL
Processed data included within Sample table

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