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Sample GSM559656 Query DataSets for GSM559656
Status Public on Jul 24, 2010
Title L-1236 siSCR rep2
Sample type RNA
 
Source name siSCR L-1236
Organism Homo sapiens
Characteristics cell line: L-1236
sirna: siSCR
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 5.843329305
7892502 6.366272235
7892503 5.593284411
7892504 9.017038177
7892505 5.810065938
7892506 6.470323422
7892507 7.017717599
7892508 7.913008587
7892509 12.23915749
7892510 6.484339167
7892511 5.901106379
7892512 7.813256288
7892513 5.68103075
7892514 10.84523441
7892515 10.04677061
7892516 6.188293232
7892517 6.383404303
7892518 5.791644179
7892519 7.572972176
7892520 9.724795338

Total number of rows: 32321

Table truncated, full table size 627 Kbytes.




Supplementary file Size Download File type/resource
GSM559656.CEL.gz 4.3 Mb (ftp)(http) CEL
Processed data included within Sample table

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