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Sample GSM141511 Query DataSets for GSM141511
Status Public on Feb 18, 2007
Title SAGE of 9-DPA fl mutant ovule
Sample type SAGE
Anchor NlaIII
Tag Count 69014
Tag Length 10
 
Source name fuzzless-lintless mutant ovule at 9 DPA
Organism Gossypium hirsutum
Characteristics 9-DPA fl mutant ovule
Treatment protocol No treatment.
Growth protocol Plants of Upland Cotton, Gossypium hirsutum L. cv. Xu-142 were grown in field. Bolls were tagged and the flowering day was taken as 0 day post-anthesis (DPA). Ovules at 9 DPA were collected in the morning, and the material was frozen in liquid nitrogen and stored at -70 C before use.
Extracted molecule total RNA
Extraction protocol Total RNA for SAGE library construction was isolated by a cold-phenol method as previously described (Li et al., 2002).
 
Description 30 μg total RNA was used to construct the SAGE library by the I-SAGE kit (Invitrogen, Carlsbad, CA) according to the manual.
Data processing The software SAGE2000 ver4.5 (courtesy of Ken Kinzler and Victor Velculescu, Johns Hopkins University School of Medicine) was applied to analyze the sequence data.
 
Submission date Oct 23, 2006
Last update date Nov 19, 2008
Contact name Xiao-Ya Chen
E-mail(s) xychen@sibs.sc.cn
Phone 86-21-54924033
Fax 86-21-54924015
URL http://xy.sippe.ac.cn/
Organization name Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences
Department Institute of Plant Physiology and Ecology
Lab National Key Laboratory of Plant Molecular Genetics
Street address No. 300, Fenglin Road
City Shanghai
ZIP/Postal code 200032
Country China
 
Platform ID GPL4474
Series (1)
GSE6103 SAGE of cotton fibers and ovules.

Data table header descriptions
TAG Ten base SAGE tag
COUNT Absolute tag count
TPM tags per million

Data table
TAG COUNT TPM
TTGTCTTGGT 1014 14692.67
CATTTTGATC 622 9012.66
CTTTGTTAAT 446 6462.46
GCTTATATGG 411 5955.31
TTTGTGAAGA 332 4810.62
TATCAACTTA 245 3550.00
TGATATGTTT 240 3477.56
TTGTCTTTTA 240 3477.56
ATTGAGTGAA 217 3144.29
CCCCTTCTTC 214 3100.82
GGGAATGAAA 214 3100.82
TCTGGTATAG 203 2941.43
AATCAATCAA 189 2738.57
TTACAGGTGA 176 2550.21
GTCAAATATG 158 2289.39
GCTGATGGTA 153 2216.94
TATCACTGTT 149 2158.98
CATAAAAAAA 149 2158.98
TTGTTGTTGT 145 2101.02
CCATCTAAGG 145 2101.02

Total number of rows: 26084

Table truncated, full table size 486 Kbytes.




Supplementary data files not provided

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