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Sample GSM590207 Query DataSets for GSM590207
Status Public on Sep 02, 2010
Title GermlineContaining_adult_totalRNA_replicate2
Sample type RNA
 
Source name mixed stage embryos from N2
Organism Caenorhabditis elegans
Characteristics strain: DH245
developmental stage: young adults
Growth protocol Worms were grown in standard S-basal media liquid culture. DH245 (fem-2 (b245)) were grown at 15C and bleached for embryos. Embryos were starved to L1 and then fed and shifted to 23C. Adults were collected over 35uM Nitex membrane, and washed with M9 and PBS. Adults were resuspended in 1 pellet volume of PBS+ protease inhibitors (Calbiochem) and frozen as ÒpopcornÓ in liquid N2, and stored at -80C. For a detailed protocol see http://www.modencode.org/.
Extracted molecule total RNA
Extraction protocol 1V sample (frozen powdered worm) in 10V Trizol that was stored at -80C was thawed at 37C. 1/5 V chloroform was added and vortexed for 30 seconds. After centrifugation at 13000 rpm for 5 minutes, aqueous phase containing RNA was recovered. RNA was precipitated by mixing with 0.8V isopropanol and incubation on ice, followed by centrifugation at 13000 rpm at 4C for 20 minutes. RNA was washed with 75% ethanol, dissolved in DEPC H2O and cleaned up using Qiagen RNeasy kit.
Label Cy3
Label protocol Cy3 Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. http://www.nimblegen.com/products/lit/index.html
 
Hybridization protocol Hybridization was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. http://www.nimblegen.com/products/lit/index.html
Scan protocol Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol.http://www.nimblegen.com/products/lit/index.html
Description Gene expression data from young feminized germline containing (fem-2) adults.
Data processing The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4 (Roche NimbleGen, Inc.).
 
Submission date Sep 02, 2010
Last update date Sep 02, 2010
Contact name Jason D Lieb
E-mail(s) jlieb@bio.unc.edu
Phone 919-843-3228
Organization name University of North Carolina at Chapel Hill
Department Biology
Lab Jason Lieb
Street address 408 Fordham Hall, CB# 3280
City Chapel Hill
State/province NC
ZIP/Postal code 27599-3280
Country USA
 
Platform ID GPL8673
Series (1)
GSE20136 Genome-wide nucleosome occupancy profiling by high throughput sequencing, and microarray analysis of RNA abundance

Data table header descriptions
ID_REF
VALUE RMA normalized transcript abundance per probe

Data table
ID_REF VALUE
2L52_1P00168 2964.08
2L52_1P00420 1549.58
2L52_1P01174 843.33
2RSSE_1P00534 457.58
2RSSE_1P00667 801.58
2RSSE_1P00891 255.33
2RSSE_2P00053 1932.83
2RSSE_2P00170 1694.58
2RSSE_2P00519 566.83
3R5_1P00138 9971.83
3R5_1P00301 4804.08
3R5_1P00585 8798.83
4R79_1aP00041 874.08
4R79_1aP00095 535.33
4R79_1aP00160 1197.83
4R79_1bP00024 883.58
4R79_1bP00221 1588.08
4R79_1bP00406 2051.58
4R79_2P00061 964.58
4R79_2P00190 1345.08

Total number of rows: 72014

Table truncated, full table size 1596 Kbytes.




Supplementary file Size Download File type/resource
GSM590207_43304102_532_AD-fem2_rep2.pair.gz 1.1 Mb (ftp)(http) PAIR
GSM590207_43304102_532_AD-fem2_rep2_RMA.calls.gz 246.7 Kb (ftp)(http) CALLS
Processed data provided as supplementary file
Processed data included within Sample table

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