2025-07-04
ENA first public
public
INSDC status
ERS25126485
SRA accession
14 days
age
HiFi_Rye_Lo7_v3
biological material ID
Germany
biological material geographic location
51,816
biological material latitude
11,283
biological material longitude
diploid
http://purl.obolibrary.org/obo/PATO_0001394
biological material ploidy
not applicable
biological material preprocessing
112m
biological  material altitude
not applicable
biological  material coordinates uncertainty
BSDC00002
checklist
2024-04-09
collection date
Secale
genus
not provided
geographic location (country and/or sea)
not collected
growth facility
HiFi
library type
not applicable
material source altitude
not applicable
material source description
not applicable
material source geographic location
not applicable
material source latitude
not applicable
material source longitude
Secale cereale
http://purl.obolibrary.org/obo/NCBITaxon_4550
organism
leaf
http://purl.obolibrary.org/obo/PO_0025034
plant anatomical entity
seedling
http://purl.obolibrary.org/obo/PO_0008037
plant structure development stage
rye Lo7 genome
project name
IPK_LIMS:3280122
sample ID
IPK_LIMS:3280123
sample ID
IPK_LIMS:3294181
sample ID
High molecular weight (HMW) DNA was extracted from a single Lo7 plant using the MACHEREY-NAGEL NucleoBond HMW DNA kit, following the manufacturer's protocol. The extracted HMW DNA was quality-controlled for concentration using the Qubit 2.0® dsDNA HS assay (Invitrogen, Waltham, USA) and for fragment size distribution using the Agilent Femto Pulse System (Agilent Technologies, Santa Clara, USA). For HiFi sequencing, the HMW DNA was fragmented into ~20 kb fragments using a Megaruptor 3 device (Diagenode) at speed setting 30. HiFi SMRTbell libraries were then prepared following the Pacific Biosciences SMRTbell Express Template Prep Kit 3.0 protocol. The final libraries were size-selected within a narrow 17-20 kb range using the SageELF system with a 0.75% Agarose Gel Cassette (Sage Science), following the manufacturer's guidelines. HiFi circular consensus sequencing (CCS) reads were generated using the PacBio Revio platform (Pacific Biosciences) in accordance with the standard operating procedure.
sample description
2024-04
sequencing date IPK
cereale
species