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Sample GSM417009 Query DataSets for GSM417009
Status Public on Nov 16, 2009
Title YPT41_totalRNA_replicate1
Sample type RNA
 
Source name mixed stage embryos from X;II fusion strain
Organism Caenorhabditis elegans
Characteristics strain: YPT41
stage: Mixed Embryos
Growth protocol Embryos were prepared by bleaching from gravid adults grown in standard S-basal media liquid culture.
Extracted molecule total RNA
Extraction protocol 1V sample in 10V Trizol that was stored at -80C was thawed at 37C, vortexed 30 seconds and re-frozen in liquid nitrogen. Freeze-cracking was repeated a total of four times. 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 mixed stage embryos isolated from YPT41, X;II fusion strain.
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 Jun 12, 2009
Last update date Nov 16, 2009
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)
GSE16621 Analysis of SDC-2, DPY-26, MIX-1, DPY-27 and RNA Polymerase II ChIP-chip and RNA abundance in C. elegans

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

Data table
ID_REF VALUE SEQ_ID
2L52_1P00168 34.56 2L52_1
2L52_1P00420 35.56 2L52_1
2L52_1P01174 39.14 2L52_1
2RSSE_1P00534 1631.44 2RSSE_1
2RSSE_1P00667 3002.45 2RSSE_1
2RSSE_1P00891 657.36 2RSSE_1
2RSSE_2P00053 4298.89 2RSSE_2
2RSSE_2P00170 4632.58 2RSSE_2
2RSSE_2P00519 2259.08 2RSSE_2
3R5_1P00138 20412.09 3R5_1
3R5_1P00301 9022.62 3R5_1
3R5_1P00585 6226.23 3R5_1
4R79_1aP00041 1946.84 4R79_1a
4R79_1aP00095 870.92 4R79_1a
4R79_1aP00160 1433.47 4R79_1a
4R79_1bP00024 3690.48 4R79_1b
4R79_1bP00221 3149.97 4R79_1b
4R79_1bP00406 5137.08 4R79_1b
4R79_2P00061 643.73 4R79_2
4R79_2P00190 954.72 4R79_2

Total number of rows: 72014

Table truncated, full table size 2248 Kbytes.




Supplementary file Size Download File type/resource
GSM417009.calls.gz 261.2 Kb (ftp)(http) CALLS
GSM417009.pair.gz 1.2 Mb (ftp)(http) PAIR
Processed data provided as supplementary file
Processed data included within Sample table

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