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Sample GSM141510 Query DataSets for GSM141510
Status Public on Feb 18, 2007
Title SAGE of 9-DPA cotton fiber
Sample type SAGE
Anchor NlaIII
Tag Count 57314
Tag Length 10
Source name Cotton fiber at 9 DPA
Organism Gossypium hirsutum
Characteristics 9-DPA cotton fiber
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 from the 9 DPA fibers by a cold-phenol method as previously described (Li et al. 2002).
Description 30 μg total RNA from 9 DPA Gossypium. hirsutum Xu-142 c.v. fiber 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
Phone 86-21-54924033
Fax 86-21-54924015
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
GAAAGTTCAC 1219 21268.80
GCTGTACTCA 741 12928.78
ATATTTATGG 375 6542.90
ATATTTATGC 356 6211.40
GCTGATGGTA 321 5600.73
CATTTTGATC 295 5147.08
TTGTCTTGGT 242 4222.35
TCCCCGTACA 238 4152.56
GATCTCCGAT 228 3978.09
GAGGAAGGAG 206 3594.24
GTTGCTTGGT 168 2931.22
AGTTTGCATA 162 2826.53
TTGATGATGA 162 2826.53
TTCTTGGTAA 157 2739.30
TTGAATTGAG 152 2652.06
GGTGGTGGTG 146 2547.37
GTTCCAGTCC 139 2425.24
ATTGAGTGAA 138 2407.79
GAATGAATGT 138 2407.79
TGGTTATTTG 126 2198.42

Total number of rows: 21905

Table truncated, full table size 408 Kbytes.

Supplementary data files not provided

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