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Sample GSM1060780 Query DataSets for GSM1060780
Status Public on Jun 12, 2013
Title SCLC237
Sample type RNA
 
Source name Small cell lung carcinoma_SCLC237
Organism Homo sapiens
Characteristics tissue: Small cell lung carcinoma
Extracted molecule total RNA
Extraction protocol Total RNAs were extracted using TRIzol (Invitrogen, Carlsbad, CA). 3 micrograms of total RNA was reverse transcribed using the SuperScript III system for cDNA synthesis (Invitrogen) according to the protocol recommended by Affymetrix. The oligonucleotide used for priming was 5'-ggccagtgaattgtaatacgactcactatagggaggcgg-(t)24-3' (Invitrogen). Double-stranded cDNA was cleaned by phenol:chloroform extraction and the aqueous phase removed by centrifugation through Phase-lock Gel (Eppendorf).
Label biotin
Label protocol In vitro transcription was performed on 1 microgram of cDNA using the Enzo BioArray High Yield RNA transcript labelling kit (Enzo Diagnostics). The cRNA was cleaned using RNAeasy clean-up columns (Qiagen). The cRNA was fragmented by heating in 40 mM Tris-acetate pH 8.1, 100 mM KOAc, 30 mM MgOAc.
 
Hybridization protocol 10 micrograms of fragmented cRNA were hybridised (45degree CelsiusC, 16 hours). Hybridization was controled by use of the GeneChip Eukaryotic Hybridization Control Kit (Affymetrix). Washing and staining was performed in a Fluidics Station 450 (Affymetrix) using the protocol EukGE-WS2v4.
Scan protocol Scanning was performed in an Affymetrix GeneChip scanner 3000 7G.
Description Small cell lung carcinoma
Data processing Genechip analysis was performed using the Affymetrix GeneChip Operating Software v1.3. Signal value was calculated using MAS5 algorithm with target intensity=100.
 
Submission date Jan 08, 2013
Last update date Jun 12, 2013
Contact name Atsushi Kaneda
E-mail(s) kaneda@genome.rcast.u-tokyo.ac.jp
Organization name The University of Tokyo
Department RCAST
Lab Genome Science Division
Street address 4-6-1 Komaba
City Meguro-ku
State/province Tokyo
ZIP/Postal code 153-8904
Country Japan
 
Platform ID GPL570
Series (2)
GSE43346 Gene repression with H3K27me3 modification in human small cell lung cancer
GSE99316 Gene repression and ChIP-seq in Human Small Cell Lung Cancer

Data table header descriptions
ID_REF
VALUE MAS5.0 signal intensity with target intensity=100

Data table
ID_REF VALUE
AFFX-BioB-5_at 9.1
AFFX-BioB-M_at 1.3
AFFX-BioB-3_at 2
AFFX-BioC-5_at 487.3
AFFX-BioC-3_at 564.2
AFFX-BioDn-5_at 2202.8
AFFX-BioDn-3_at 5259
AFFX-CreX-5_at 10082.2
AFFX-CreX-3_at 12618.8
AFFX-DapX-5_at 5.9
AFFX-DapX-M_at 8.2
AFFX-DapX-3_at 1.1
AFFX-LysX-5_at 1
AFFX-LysX-M_at 1.7
AFFX-LysX-3_at 4.7
AFFX-PheX-5_at 1.8
AFFX-PheX-M_at 0.8
AFFX-PheX-3_at 12.1
AFFX-ThrX-5_at 12.5
AFFX-ThrX-M_at 6.9

Total number of rows: 54675

Table truncated, full table size 833 Kbytes.




Supplementary file Size Download File type/resource
GSM1060780_SCLC237_U133p2.CEL.gz 7.6 Mb (ftp)(http) CEL
Processed data included within Sample table

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