E-GEOD-37125 - non-coding RNA sequencing of upland cotton fiber and ovule

Status
Released on 6 June 2012, last updated on 11 March 2013
Organism
Gossypium hirsutum
Samples (4)
Protocols (3)
Description
Three samples of cotton fiber harvested 3, 7 and 15 days post anthesis (DPA) and a sample of cotton ovule harvestd 0 DPA were used for non-coding RNA extraction and seloxa sequencing experiments, respectively.Cotton plants (Gossypium hirsutum cv. Xuzhou 142) were grown in a soil mixture in fully automated walk-in growth rooms with 300 µmol m–2 s–1 average light intensity, 60% relative humidity and temperatures set to 30C during the light period and 28C during the dark (12-h light/dark cycle). These conditions were consistent throughout the year. Small RNA molecules under 30 bases were amplified and isolated from an agarose gel. The purified DNA was used directly for cluster generation and sequencing analysis using the Illumina Genome Analyzer IIx according to the manufacturer's instructions. The 38nt sequence tags from sequencing went through data cleaning first, which included getting rid of the low-quality tags and clipping adapter sequences. Three samples of cotton fiber harvested 3, 7 and 15 days post anthesis (DPA) and a sample of cotton ovule harvestd 0 DPA were used for non-coding RNA extraction and seloxa sequencing experiments, respectively.
Experiment type
RNA-seq of non coding RNA 
Contacts
Yu-Xian Zhu <zhuyx@water.pku.edu.cn>, Guang-hui Xiao, Qin Li, Xiang Jin, Yu-xian Zhu
MINSEQE
Exp. designProtocolsFactorsProcessedSeq. reads
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