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Sample GSM1034127 Query DataSets for GSM1034127
Status Public on Nov 10, 2012
Title SC-1 control REP1
Sample type RNA
 
Source name DLBCL cell line SC-1 stably transfected with a tetracycline-inducible LITAF expression vector, absence of doxycycline
Organism Homo sapiens
Characteristics cell line: SC-1
cell type: diffuse large B-cell lymphoma (DLBCL) cells stably transfected with a tetracycline-inducible LITAF expression vector
treatment: none
Treatment protocol Absence or presence of 4 mg/ml doxycycline for LITAF over-expression. Nucleofection (AMAXA) with Silencer Select Negative Control No. 1 (AM4611, Invitrogen) or a LITAF-specific siRNA (s18252, Invitrogen) for silencing. RNA was extracted 48h after the treatment.
Growth protocol Cell lines were grown at 37ºC and 5% CO2 in RPMI 1640 supplemented with 10% fetal bovine serum, 100 units/mL of penicillin and 100 mg/mL of streptomycin.
Extracted molecule total RNA
Extraction protocol The cells were harvested with TRIzol Reagent (Invitrogen) and the RNA was extracted according to the manufacturer's instructions. As a last step of the extraction procedure, the RNA was purified with the RNeasy Mini-kit (Qiagen, Hilden, Germany).
Label Biotin
Label protocol The cDNA was prepared from 2 microg total RNA using the One-Cycle cDNA Synthesis kit from Affymetrix. This cDNA was used for synthesizing the cRNA using the IVT labeling kit (Affymetrix). The synthesized cRNA was purified with the GeneChip Sample Cleanup Module (Affymetrix).
 
Hybridization protocol Following fragmentation, 15 microg of cRNA were hybridized to the Affymetrix HG-U133 Plus 2.0 chip according to the protocols provided by the manufacturer.
Scan protocol GeneChips were scanned using the GeneChip Scanner 3000 from Affymetrix.
Description SC1_LITAF_CTRL_R1
Gene expression data from a DLBCL cell line.
Data processing Data were normalized with Bioconductor software using the RMA algorithm.
 
Submission date Nov 08, 2012
Last update date Nov 10, 2012
Contact name Raquel Malumbres
E-mail(s) rmalumbres@yahoo.com
Phone +34 948194700
Organization name University of Navarra/ Clínica Universidad de Navarra
Department Hemato-Oncology
Lab Multiple Myeloma
Street address Avenida Pio XII 55
City Pamplona
State/province Navarra
ZIP/Postal code 31008
Country Spain
 
Platform ID GPL570
Series (2)
GSE42174 Global expression analysis of DLBCL cell lines with LITAF over-expression or silencing
GSE42204 LITAF, a BCL6 target gene, regulates autophagy in mature B-cell lymphomas

Data table header descriptions
ID_REF
VALUE RMA signal

Data table
ID_REF VALUE
1007_s_at 202.6827942
1053_at 897.003161
117_at 15.90567261
121_at 118.8516372
1255_g_at 5.534526758
1294_at 24.05593908
1316_at 22.1227047
1320_at 7.039724495
1405_i_at 5.934533488
1431_at 10.29807784
1438_at 16.49448616
1487_at 154.7124412
1494_f_at 29.47879572
1552256_a_at 223.4156097
1552257_a_at 560.7763631
1552258_at 13.13605883
1552261_at 8.047572318
1552263_at 106.3082745
1552264_a_at 152.5741531
1552266_at 6.499585501

Total number of rows: 54675

Table truncated, full table size 1212 Kbytes.




Supplementary file Size Download File type/resource
GSM1034127_SC_1_LITAF_CTRL_R1.CEL.gz 4.5 Mb (ftp)(http) CEL
Processed data included within Sample table

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