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Sample GSM1098566 Query DataSets for GSM1098566
Status Public on Nov 15, 2013
Title DMS-273 rep2
Sample type RNA
 
Channel 1
Source name Pooled clone 30 DMS-272
Organism Homo sapiens
Characteristics treatment: SETDB1 KD
cell line: DMS-273 SCLC
tissue: Lung
Growth protocol Total RNA fraction. RNA Integrity Numbers were in the range 9.3 to 10.0 when assayed by Lab-chip technology on an Agilent 2100 Bioanalyzer.
Extracted molecule total RNA
Extraction protocol Trizol
Label Cy5
Label protocol Amount of nucleic acid labeled: 100ng. Commercial Two-Color Microarray-Based Gene Expression Analysis (Low Input Quick Amp Labeling) version 6.5 kit by following manufacturer instructions. Agilent manual G4140-90050 of May 2010. Amplification: by RNA polymerases. Briefly, MMLV-RT retrotranscription of sample from a T7 promoter primer is followed by a T7 RNA pol catalysed in vitro transcription reaction in the presence of either Cy3-CTP or Cy5-CTP fluorophores. Labeled samples are purified with silica-based RNeasy spin columns (Qiagen).
 
Channel 2
Source name DMS-273 Control
Organism Homo sapiens
Characteristics treatment: scrambled
cell line: DMS-273 SCLC
tissue: Lung
Growth protocol Total RNA fraction. RNA Integrity Numbers were in the range 9.3 to 10.0 when assayed by Lab-chip technology on an Agilent 2100 Bioanalyzer.
Extracted molecule total RNA
Extraction protocol Trizol
Label Cy3
Label protocol Amount of nucleic acid labeled: 100ng. Commercial Two-Color Microarray-Based Gene Expression Analysis (Low Input Quick Amp Labeling) version 6.5 kit by following manufacturer instructions. Agilent manual G4140-90050 of May 2010. Amplification: by RNA polymerases. Briefly, MMLV-RT retrotranscription of sample from a T7 promoter primer is followed by a T7 RNA pol catalysed in vitro transcription reaction in the presence of either Cy3-CTP or Cy5-CTP fluorophores. Labeled samples are purified with silica-based RNeasy spin columns (Qiagen).
 
 
Hybridization protocol Hybridization chamber type: SureHyb hybridization chamber (Agilent). Quantity of each labeled extract used: 300 ng. Volume: 50 uL. Temperature (ÂșC): 65. Duration: 17 hours.
Scan protocol Scanned on an G2505C DNA microarray scanner (Agilent). Images were analysed by Agilent Feature Extraction Software (ver. 10.7), which performed feature quantitation and additive detrend correction. No background subtraction was performed.
Description DMS-273 Control
Data processing Data from hybridised microarray images were quantitated, corrected by additive detrending and submitted to dye bias normalisation after bias detection by linear and Lowess curve fitting methods (Agilent FeatureExtraction (FE) Software).Raw data signals are thresholded to 1, and replicated probe signals for the individual channels (Cy5 and Cy3) are summarized by computing their geometric mean. Normalised signal values are obtained by Cy5/Cy3 ratio computing and Log base2 transformation. These manipulations are done with GeneSpring GX12 software.
 
Submission date Mar 14, 2013
Last update date Apr 23, 2018
Contact name Manel Esteller
Organization name IDIBELL
Department PEBC
Lab Cancer Epigenetics
Street address Hospital Duran i Reynals Av. Gran Via s/n km, 2.7
City L'Hospitalet de Llobregat
State/province Barcelona
ZIP/Postal code 08908
Country Spain
 
Platform ID GPL17077
Series (1)
GSE45175 Human lung cancer cell lines DMS-273 (SCLC) and NCI-H1437 (NSCLC): scrambled vs. shRNA clones
Relations
Reanalyzed by GSE113533

Data table header descriptions
ID_REF
VALUE Normalised [Log (Cy5/Cy3)] representing 'Cy5'/'Cy3' signal ratios.

Data table
ID_REF VALUE
A_19_P00315452 1.866123684
A_19_P00315459 -0.143254227
A_19_P00315482 0.153422166
A_19_P00315492 -0.169470681
A_19_P00315493 0.190407948
A_19_P00315502 -0.349362297
A_19_P00315506 -0.099772103
A_19_P00315518 -0.381966808
A_19_P00315519 -0.031889071
A_19_P00315524 -0.33337076
A_19_P00315528 -0.198653334
A_19_P00315529 -0.124027252
A_19_P00315538 0.278405035
A_19_P00315541 -0.381966808
A_19_P00315543 -0.259230093
A_19_P00315550 -0.489332692
A_19_P00315551 0.135609357
A_19_P00315554 0.569661531
A_19_P00315581 0.747610265
A_19_P00315583 -0.121509023

Total number of rows: 50599

Table truncated, full table size 1279 Kbytes.




Supplementary file Size Download File type/resource
GSM1098566_US22502553_253949411170_S01_GE2_1100_Jul11_B_1_1.txt.gz 5.8 Mb (ftp)(http) TXT
Processed data included within Sample table

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