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Sample GSM343393 Query DataSets for GSM343393
Status Public on Jan 16, 2009
Title HeLa_siDicer_24_rep2
Sample type RNA
 
Source name HeLa total RNA, 24hrs after transfection of siRNA against Dicer
Organism Homo sapiens
Characteristics Cervical cancer cell line
Treatment protocol 32nM of siRNAs (Samchully Phamaceuticals) were transfected into HeLa cells with lipofectamine 2000 (InvitroGen).
Growth protocol HeLa cells were cultured in DMEM supplemented with 10% FBS.
Extracted molecule total RNA
Extraction protocol Trizol extraction of total RNA was performed according to manufacturer's instructions.
Label biotin
Label protocol Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (Wt_sensetarget_label_manual(updated manual)_1, 2007, Affymetrix).
 
Hybridization protocol Following fragmentation, 2.3 ug of cDNA were hybridized for 17 hr at 45C on GeneChip Human Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450. Hybridization cocktails containing 5 to 5.5 µg of fragmented, end-labeled single-stranded cDNA were prepared and hybridized to GeneChip Human gene 1.0 ST arrays
Scan protocol GeneChips were scanned using the GeneChip Scanner 3000 7G.
Description Expression changes of HeLa mRNA after Dicer knockdown for 24hrs
Data processing All gene array data was analyzed using tools in Expression consol software (Affymetrix). The Robust Multi-array Analysis (RMA) (Irizarry, Hobbs, Collin, Beazer-Barclay, Antonellis, Scherf, and Speed 2003) algorithm was used for probeset (gene-level) intensity analysis.
 
Submission date Nov 18, 2008
Last update date Jan 16, 2009
Contact name Jinju Han
Organization name Seoul National University
Lab Bd. 504, Rm 501
Street address 599 Gwanangno, Gwanak-gu
City Seoul
ZIP/Postal code 151-742
Country South Korea
 
Platform ID GPL6244
Series (2)
GSE13638 Ago2 or Dicer knockdown effects on mRNA levels in HeLa
GSE13640 Effect of miRNA biogenesis factors on mRNA levels

Data table header descriptions
ID_REF
VALUE RMA processed signal

Data table
ID_REF VALUE
7896738 2.554048
7896740 3.318328
7896742 7.383775
7896744 7.27254
7896746 9.110426
7896748 9.489309
7896750 4.195046
7896752 9.522193
7896754 6.854032
7896756 4.883184
7896759 6.487741
7896761 7.203957
7896779 6.978673
7896798 6.439692
7896817 6.422925
7896822 8.068554
7896859 5.19086
7896861 3.26864
7896863 5.697608
7896865 6.377892

Total number of rows: 33297

Table truncated, full table size 549 Kbytes.




Supplementary file Size Download File type/resource
GSM343393.CEL.gz 4.0 Mb (ftp)(http) CEL
Processed data included within Sample table

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