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Sample GSM559661 Query DataSets for GSM559661
Status Public on Jul 24, 2010
Title L-UHO-1 siGATA-3 rep1
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 6.230479706
7892502 6.378181938
7892503 5.32558297
7892504 9.743841643
7892505 5.646148768
7892506 6.685826163
7892507 7.029700463
7892508 8.081154294
7892509 12.07788355
7892510 6.18341289
7892511 5.515638413
7892512 7.582337752
7892513 5.626639839
7892514 11.4903916
7892515 10.02543783
7892516 6.585308984
7892517 6.494353379
7892518 5.478516399
7892519 6.954964924
7892520 9.819690248

Total number of rows: 32321

Table truncated, full table size 627 Kbytes.




Supplementary file Size Download File type/resource
GSM559661.CEL.gz 4.2 Mb (ftp)(http) CEL
Processed data included within Sample table

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