SAMN02227984
External Id
Michael Axtell Lab, Pennsylvania State University
INSDC center name
2013-07-08T00:00:00Z
INSDC first public
2021-02-28T02:07:34.526Z
INSDC last update
SRS458047
INSDC secondary accession
live
INSDC status
Generic
NCBI submission model
Generic.1.0
NCBI submission package
SRS458047
SRA accession
4 weeks
http://purl.obolibrary.org/obo/UO_0000034
age
2010-12-15
collection date
Columbia (Col-0)
http://www.ebi.ac.uk/efo/EFO_0005148
cultivar
Genomic DNA was extracted from wild-type Arabidopsis thaliana Col-0 leaves using Nucleon PhytoPure Genomic DNA Extraction Kits (GE Healthcare). 100 ug genomic DNA (100 ul @ 1 ug/ 1ul), 300 ul Hybridization Buffer P5 (Invitrogen) and 1 pmole LNA-biotinylated capture probe (1 ul @ 1uM) were placed in a 1.7 ml centrifuge tube and boiled for 5 minutes to denature the genomic DNA. The mix was placed in 45C for 30 minutes for hybridization. 20 ul streptavidin beads from the RiboMinus Plant Kit (Invitrogen) were prepared per the manufacturer's protocol. After 30 minutes of hybridization, the hybridization mix was added to the beads and incubated at 45C for 15 minutes with occasional (every 2-3 minutes) gentle mixing by inversion. Beads were captured with a magnetic stand and were washed 3 times each for 2 minutes with 500 ul 0.1X SSC incubated at 45C. Captured DNA was eluted for one minute with 500 ul nanopure water at 90C twice. DNA was mixed with 1/10 volume 3M sodium acetate pH 5.2, 20 ug glycogen (1 ul @ 20 ug/ul) and 3 volumes of 95% ethanol, vortexed for 30 seconds, and then placed at -20C overnight for ethanol precipitation. DNA was centrifuged at maximum speed at 4C for 20 minutes to spin down pellets. Pellets were washed by 75% ethanol and centrifuged at maximum speed at 4C for 5 minutes and air dried at 4C. DNA was then resuspended in a minimal volume (4-8 ul) of nanopure water. DNA was linearly amplified with the illustra GenomiPhi V2 DNA Amplification Kit (GE Healthcare) per the manufacturer's protocol, with the only modification that the incubation time was increased from 1.5 hours to 2 hours.
description
wild type
http://www.ebi.ac.uk/efo/EFO_0005168
genotype
USA: Columbia
geo loc name
wild-type plants growing in a growth room
isolation source
Arabidopsis thaliana
http://purl.obolibrary.org/obo/NCBITaxon_3702
organism
leaf
http://purl.obolibrary.org/obo/PO_0025034
tissue type
General Sample for Arabidopsis thaliana
title