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Sample GSM153402 Query DataSets for GSM153402
Status Public on Nov 11, 2007
Title NELF-depleted 0612_Dm_S2_NELF-depleted_1
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, 96 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 96 hours, as described in Armknecht, S. et al. (2005) Methods in Enzymology, 392: pp. 55-79
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 6.0). 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 Dec 26, 2006
Last update date Aug 28, 2018
Contact name NIEHS Microarray Core
E-mail(s) [email protected], [email protected]
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)
GSE6714 RNA polymerase is poised for activation across the genome
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
1627418_at 2.9016
1641695_a_at 1.74048
1626371_at 11.42119
1635135_at 8.13074
1628120_at 2.01348
1633391_at 11.20372
1627492_at 7.98501
AFFX-Dm-Q9LK88_at 3.84945
1625443_a_at 9.4057
1632911_at
1636559_s_at 11.17846
1632158_a_at 8.90363
1637736_a_at 7.88416
1636844_at 8.0251
1641229_at
1637852_at
1637522_at
1632875_at 7.48439
1625199_s_at 9.2629
1635424_s_at

Total number of rows: 15939

Table truncated, full table size 290 Kbytes.




Supplementary file Size Download File type/resource
GSM153402.CEL.gz 2.1 Mb (ftp)(http) CEL

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