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Sample GSM1429323 Query DataSets for GSM1429323
Status Public on Oct 07, 2015
Title HCC33_shRNA5
Sample type RNA
Source name Small Cell Lung Cancer (SCLC)
Organism Homo sapiens
Characteristics cell line: HCC33
shRNA: transfected with short hairpin RNA number 5, against KAT6B gene
Treatment protocol Not special additional treatment
Growth protocol Cells where growth on RPMI media with 10% FBS, 1% PS
Extracted molecule total RNA
Extraction protocol Total mRNA was extrated using Trizol Reagent.
Label Cy3
Label protocol Amount of nucleic acid labeled: 100ng. Commercial One-Color Microarray-Based Gene Expression Analysis (Low Input Quick Amp Labeling) version 6.5 kit by following manufacturer instructions. Agilent manual G4140-90040 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 Cy3-CTP fluorophore. Labeled samples are purified with silica-based spin columns.
Hybridization protocol Microarray: Human Gene Expression G3 v2 60K (Agilent microarray design ID 039494, P/N G4851B). Microarray sequences and annotations are listed in sheet '039494_hg19_20120628'. Hybridization chamber type: SureHyb hybridization chamber (Agilent). Quantity of labeled extract used: 600 ng. Volume: 50 µL. Temperature (ºC): 65. Duration: 17 hours.
Scan protocol Scanned on an G2505C DNA microarray scanner (Agilent).
Description HCC33 cell line transfected with short hairpin RNA number 5, against KAT6B gene
Data processing Images were analysed by Agilent Feature Extraction Software (ver. 11.5), which performed feature quantitation and additive detrend correction. No background subtraction was performed.
Submission date Jul 07, 2014
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 (2)
GSE59136 Identification of KAT6B signature on KAT6B deficient SCLC cell Lines
GSE62775 KAT6B gene deletion as a predictive biomarker to Irinotecan response in small cell lung cancer
Reanalyzed by GSE113533

Data table header descriptions
VALUE Normalized signal intensity

Data table
GE_BrightCorner 16.1923125
DarkCorner 4.790450453
A_23_P117082 11.56737734
A_33_P3246448 4.924941891
A_33_P3318220 4.826686994
A_33_P3236322 5.337719094
A_33_P3319925 5.266888623
A_21_P0000509 14.18029791
A_21_P0000744 10.49941264
A_24_P215804 6.914417715
A_23_P110167 9.535896595
A_33_P3211513 8.067449012
A_23_P103349 5.124825438
A_32_P61480 5.111249382
A_33_P3788124 4.97740469
A_33_P3414202 8.85565565
A_33_P3316686 7.413122045
A_33_P3300975 5.111249382
A_33_P3263061 11.75104825
A_33_P3261373 5.071579245

Total number of rows: 50739

Table truncated, full table size 1260 Kbytes.

Supplementary file Size Download File type/resource
GSM1429323_253949430077_S01_GE1_1105_Oct12_B_1_3.txt.gz 3.0 Mb (ftp)(http) TXT
Processed data included within Sample table

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