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SRX691585: GSM1496102: Col20GC2; Arabidopsis thaliana; RNA-Seq
1 ILLUMINA (Illumina HiSeq 2000) run: 40.6M spots, 6.9G bases, 3.3Gb downloads

Submitted by: Gene Expression Omnibus (GEO)
Study: Dormancy of green-cotyledon Col seeds matured at 20°C vs 15°C
show Abstracthide Abstract
To determine genes involved in induction of dormancy in response to reduced maturation temperatures, RNA sequencing was performed on developing seeds matured at 20°C, where low dormancy is observed, and compared to seeds matured at 15°C where high dormancy is observed. Overall design: Col green cotyledon seeds matured at 20°C and 15°C were dissected from siliques between five to seven hours after dawn and frozen in liquid nitrogen. RNA was extracted as described previously (Penfield et al., 2005).
Sample: Col20GC2
SAMN03018420 • SRS693852 • All experiments • All runs
Instrument: Illumina HiSeq 2000
Strategy: RNA-Seq
Selection: cDNA
Layout: SINGLE
Construction protocol: 150 mg of seed (based on dry seed weight) was ground and extracted with 1 ml of frozen XT buffer (0.2M sodium borate, 30 mM EGTA, 1% SDS, 1% sodium deoxycholate, 2% polyvinylpyrollidone, 10 mM DTT, and 1% IGEPAL [pH 9.0]) in a pestle and mortar. This was allowed to thaw and was treated with 40 μl proteinase K (PCR grade, Roche, UK) for 90 min at 42°C; precipitation on ice followed for 1 hr with 80 μl 2M potassium chloride. The supernatant was collected after centrifugation at 4°C. The RNA was precipitated from the supernatant at −20°C for 2 hr with 360 μl 8M lithium chloride. The RNA was collected by centrifugation at 4°C and redissolved in 100 μl water. The RNA was further purified via the clean-up protocol of the RNeasy Plant RNA isolation kit (Qiagen) according to the manufacturer's protocol. 5 μg RNA was submitted to sequencing using standard protocols for Illumina TruSeq™ technologies RS-122-2001 | TruSeq™ RNA Sample Prep Kit v2. Data were generated on Illumina HiSeq 2000. The input material contains 1-2% PhiX which is used as a control.
Experiment attributes:
GEO Accession: GSM1496102
External link:
Runs: 1 run, 40.6M spots, 6.9G bases, 3.3Gb
Run# of Spots# of BasesSizePublished


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