characteristics.text: SAMN00000756
characteristics.characteristic: External Id
characteristics.text: University of Illinois at Urbana-Champaign
characteristics.characteristic: INSDC center name
characteristics.text: 2008-10-24T11:37:43.180Z
characteristics.characteristic: INSDC first public
characteristics.text: 2013-06-12T08:43:01.467Z
characteristics.characteristic: INSDC last update
characteristics.text: SRS001217
characteristics.characteristic: INSDC secondary accession
characteristics.text: live
characteristics.characteristic: INSDC status
characteristics.text: Generic
characteristics.characteristic: NCBI submission model
characteristics.text: Generic.1.0
characteristics.characteristic: NCBI submission package
characteristics.text: SRS001217
characteristics.characteristic: SRA accession
characteristics.text: The genomic DNA sequence comes from the nematode Heterodera glycines, the common name is the soybean cyst nematode. DNA sequence data collected from strain of the nematode, called TN10. Nematode DNA was extracted from frozen second-stage juveniles of the soybean cyst nematode, species Heterodera glycines. A standard Proteinase K with phenol-chloroform extraction method was used (see details below). SCN eggs were harvested as described in Niblack (1993). Eggs were deposited on top of an egg hatching apparatus consisting of 41 micron mesh sieve held taut between 2 stacked 50 ml polypropylene beakers with there bottoms cut off. The bottom surface of the sieve cloth was carefully laid on top of a shallow layer of sterile dH20 containing 1%streptomycin sulfate solution (Sigma) in a 60mm petri dish bottom. As the second-stage juveniles (J2s) hatched, they crawled through the mesh to the liquid in the petri dish. The clean J2s were collected from the petri dish after allowing the J2 to accumulate for 24 hours. The J2s were concentrated by centrifugation until a 250 ul packed J2 pellet was obtained, then the J2's were flash frozen in liquid nitrogen. The frozen J2 pellet was transferred to a tissue publverizer (Fisher Scientific) precooled in liquid nitrogen and crushed. The pulverized frozen nematode fragments were mixed with 2 ml of proteinase K solution (0.1M Tris-HCl (pH 8.0), 1 mM EDTA, 0.15M NaCl, 1% sodium dodecyl sulfate, 1mM dithiothreitol, 2 mg/ml proteinase K) and were incubated for one hour at 37C. The DNA was phenol/chloroform-extracted, then ethanol precipitated as described in (Sambrook et al. 1989). The DNA was resuspended in 1 ml of TE (10 mM Tris-HCl pH 8, EDTA pH 8) containing RNase A at 10 microgram per ml and incubated at 37 degrees C for one hour. The DNA was next diluted to 20ml with column buffer (750 mM NaCl; 50mM MOPS , pH 7; 15% isopropanol, 0.15% Triton X-100) and then further purified on a Genomic-tip 500/G as described in the manufacturers protocol (Qiagen, Valencia, CA). The eluted SCN genomic DNA was concentrated by ethanol precipitation and resuspended in 200 ul of TE.
characteristics.characteristic: description
characteristics.text: Heterodera glycines
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/NCBITaxon_51029
characteristics.characteristic: organism
characteristics.text: TN10
characteristics.characteristic: strain
characteristics.text: Generic sample from Heterodera glycines
characteristics.characteristic: title