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Sample GSM559657 Query DataSets for GSM559657
Status Public on Jul 24, 2010
Title L-1236 siGATA-3 rep2
Sample type RNA
 
Source name siGATA-3 L-1236
Organism Homo sapiens
Characteristics cell line: L-1236
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 5.743170285
7892502 6.816949487
7892503 5.365675779
7892504 9.208574117
7892505 5.667605755
7892506 6.35725603
7892507 6.643191788
7892508 7.391129205
7892509 12.040274
7892510 6.406281847
7892511 5.757548586
7892512 8.01423045
7892513 5.972331122
7892514 10.91555653
7892515 9.995554777
7892516 6.817545459
7892517 6.105571401
7892518 5.836747034
7892519 7.528097927
7892520 9.695324993

Total number of rows: 32321

Table truncated, full table size 627 Kbytes.




Supplementary file Size Download File type/resource
GSM559657.CEL.gz 4.3 Mb (ftp)(http) CEL
Processed data included within Sample table

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