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Sample GSM170919 Query DataSets for GSM170919
Status Public on Feb 23, 2007
Title SNU library
Sample type MPSS
 
Source name Germinating seedlings
Organism Oryza sativa
Characteristics Cultivar: Nipponbare
Germinating seedlings
Extracted molecule total RNA
Extraction protocol Total RNA was isolated using TRIzol reagent.
 
Description All MPSS was performed essentially as described by Brenner et al. (Nat Biotechnol. 2000 18:630).
The specific modifications to the method for the MPSS sequencing of small RNAs are described in the paper Lu et al. (Science 2005, 309:1567) .
Data processing To determine the normalized abundance value for each signature in the library, we separately merged 2-step runs and 3-step runs to create a raw abundance count for each stepper. The average total number of signatures sequenced in all 2-step or for all 3-step runs was calculated within the library. The normalized abundance is the raw abundance count divided by the average total number of signatures for both of the steppers in the library, multiplied by 250,000 to obtain a "transcripts per quarter million" or TPQ value. For each signature, only one normalized value is used - either the 2-step or 3-step normalized value, selected based on the higher of the sum of the 2-step or 3-step data across all libraries. The numbers in the VALUE column represent the expression level of the corresponding signatures in the SNU libraries. More details are available in Meyers et al. (2004, Genome Research 14:1641).
 
Submission date Feb 22, 2007
Last update date Feb 22, 2007
Contact name Blake C. Meyers
E-mail(s) bmeyers@danforthcenter.org
Phone 314-587-1422
Organization name Donald Danforth Plant Science Center
Lab Meyers lab
Street address 975 N Warson Road
City St. Louis
State/province MO
ZIP/Postal code 63132
Country USA
 
Platform ID GPL3776
Series (1)
GSE7107 An expression atlas of rice mRNAs and small RNAs

Data table header descriptions
ID_REF
VALUE Normalized expression value

Data table
ID_REF VALUE
AAACAGTGAGCCCATGC 1
AAACAGTGGATCAGGAG 1
AAACAGTGTGCGTATGG 11
AAACATACACAGGTGTT 15
AAACATACTCAAGATCA 1
AAACATATCGGGATTCG 1
AAACATCACATCGAATC 6
AAACATCAGGAGCAGTT 2
AAACATCCGATATGACA 1
AAACATCCGATCTTTAG 5
AAACATCGGACGCCTAT 1
AAACATGTCCAGATTCA 1
AAACATTCAAGCCATCC 2
AAACATTCGATGTGACA 2
AAACATTCGATGTGATA 7
AAACATTGGGCACGAAA 3
AAACATTGGGTCCCTGC 3
AAACATTGGGTTACATC 6
AAACATTTATCGCTAAA 1
AAACCAACCTAGATTGG 2

Total number of rows: 33115

Table truncated, full table size 653 Kbytes.




Supplementary data files not provided

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