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Sample GSM142339 Query DataSets for GSM142339
Status Public on Jul 14, 2008
Title NELF depleted 0610_Dm_S2_NELF-depleted_2
Sample type RNA
 
Source name Drosophila melanogaster S2 cells that have been depleted of the NELF complex using dsRNA targeting NELF-B and NELF-E, 72 hour treatment
Organism Drosophila melanogaster
Characteristics Drosophila melanogaster S2 cells, male, largely tetraploid
Biomaterial provider Drosophila melanogaster S2 cells were obtained from the Drosophila Genomics Resource Center
Treatment protocol Cells were untreated, or treated with dsRNA for 72 hours, as described in Armknecht, S. et al. (2005) Methods in Enzymology, 392: pp. 55-80
Growth protocol Cells were grown in Shields and Sang medium, supplemented with bactopeptone and yeast extract, plus 10% Fetal Bovine Serum, as recommended by the Drosophila Genomics Resource Center
Extracted molecule total RNA
Extraction protocol The RNeasy RNA extraction kit, with on column DNAse digestion (Qiagen) was used, according to manufacturer’s protocol.
Label biotin
Label protocol Starting with 1ug of total RNA, biotin-labeled cRNA was produced using the Affymetrix 3’ Amplification One-Cycle Target labeling kit according to manufacturer’s protocol.
 
Hybridization protocol 10ug of amplified cRNAs were fragmented and hybridized to the array for 16 hours in a rotating hybridization oven using the Affymetrix Eukaryotic Target Hybridization Controls and protocol.
Scan protocol Slides were stained and washed as indicated in the Antibody Amplification Stain for Eukaryotic Targets protocol using the Affymetrix Fluidics Station FS450. Arrays were then scanned with an Affymetrix Scanner 3000 and data was obtained using the Genechip® Operating Software (Version 1.2.0.037).
Description Gene expression analysis was conducted using Drosophila Genome 2.0 Genechip® arrays (Affymetrix, Santa Clara, CA). Starting with 1ug of total RNA, biotin-labeled cRNA was produced using the Affymetrix 3’ Amplification One-Cycle Target labeling kit according to manufacturer’s protocol. For each array, 10ug of amplified cRNAs were fragmented and hybridized to the array for 16 hours in a rotating hybridization oven using the Affymetrix Eukaryotic Target Hybridization Controls and protocol. Slides were stained and washed as indicated in the Antibody Amplification Stain for Eukaryotic Targets protocol using the Affymetrix Fluidics Station FS450. Arrays were then scanned with an Affymetrix Scanner 3000 and data was obtained using the Genechip® Operating Software (Version 1.2.0.037).
Data processing The resulting files (.dat, .cel and .chp) were imported into the Rosetta Resolver system (Version 5.1). This system performs data pre-processing and error modeling as described in Weng (2004). Resolver generated fold-changes and p values, based on ratios built in the system, were exported for further analysis.
 
Submission date Oct 25, 2006
Last update date Aug 28, 2018
Contact name NIEHS Microarray Core
E-mail(s) microarray@niehs.nih.gov, liuliw@niehs.nih.gov
Organization name NIEHS
Department DIR
Lab Microarray Core
Street address 111 T.W. Alexander Drive
City RTP
State/province NC
ZIP/Postal code 27709
Country USA
 
Platform ID GPL1322
Series (1)
GSE6141 Global Analysis of the Drosophila NELF complex
Relations
Reanalyzed by GSE119084

Data table header descriptions
ID_REF probeset IDs from the Affymetrix Drosophila Genome 2.0 array
VALUE Rosetta Resolver Error Model, log2 Intensity

Data table
ID_REF VALUE
1641695_a_at 1.37208
1626371_at 11.35472
1635135_at 7.57209
1628120_at 2.59887
1633391_at 10.8852
1625782_at 0.13307
1627492_at 6.90012
AFFX-Dm-Q9LK88_at 2.47686
1625443_a_at 9.74581
1636559_s_at 11.10474
1632158_a_at 8.20635
1637736_a_at 6.75611
1636844_at 7.51076
1641229_at 2.8942
1637522_at 0.24575
1628800_at 0.04037
1632875_at 6.95982
1625199_s_at 9.05411
1635424_s_at 2.00084
1624943_at 3.9802

Total number of rows: 14146

Table truncated, full table size 268 Kbytes.




Supplementary file Size Download File type/resource
GSM142339.CEL.gz 1.9 Mb (ftp)(http) CEL

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