characteristics.text: SAMN41656423
characteristics.characteristic: External Id
characteristics.text: Georgia Institute of Technology
characteristics.characteristic: INSDC center name
characteristics.text: 2024-06-03T00:00:00Z
characteristics.characteristic: INSDC first public
characteristics.text: 2024-06-03T12:01:11.990Z
characteristics.characteristic: INSDC last update
characteristics.text: SRS21499479
characteristics.characteristic: INSDC secondary accession
characteristics.text: live
characteristics.characteristic: INSDC status
characteristics.text: MIGS/MIMS/MIMARKS.human-associated
characteristics.characteristic: NCBI submission model
characteristics.text: MIGS.ba
characteristics.characteristic: NCBI submission model
characteristics.text: MIGS.ba.human-associated.6.0
characteristics.characteristic: NCBI submission package
characteristics.text: SRS21499479
characteristics.characteristic: SRA accession
characteristics.text: 2019-09-17
characteristics.characteristic: collection_date
characteristics.text: Samples were obtained from the clinical that and had previously been processed by decontamination to reduced non-Mycobacterial species, grown in nonradiometric mycobacteria growth indicator tube (MGIT), and provided as streaks on Lowenstein Jensen agar slants. followed by Mycobacterium abscessus confirmation testing on a representative isolate. Isolates were streaked on 7H11 agar and representative colonies isolated after 5-7 days of incubation, cultured, and stocked. Stocks were stored in 12% glycerol at -80˚C. For use isolates were streaked from freezer stocks on 7H11 grown for 3-5 days at 37˚C then cultures grown in 7H9 supplemented with glycerol, OADC, and 0.05% tween 80. Morphotyping was done by visual examination on the primary streak plate. If multiple colony morphotypes were present, they were isolated and stocked. Isolates were grown from a single colony in 10mls. Cultures were centrifuged and DNA isolated using the MasterPure Gram Positive DNA Purification kit (Lucigen) with modifications*. Briefly, bacteria were resuspended in TE, transferred to Lysis Matrix B tubes, and 2 l of lysozyme added and incubated for 1 hour at 37˚C. GP lysis solution was added at 300 l per sample and tubed bead beat 3 time for 45 seconds each, placing the samples on ice to cool after each bead beating interval. Next 2 l of proteinase K was added, heated to 65-70˚C for 15 minutes, the incubated at 55˚C for 2 hours. Samples were cooled to 37C, 350ul of MPC Protein and vortexed. Debris was pelleted by centrifugation at 4˚C for 10 minutes at >10,000 x g. To further remove debris supernatant was transfer to a new tube and recentrifuged before transferring to a fresh tube. Samples were depleted of RNA using 2 l of RNaseA and incubating at 37˚C for 30 minutes. The resulting DNA was precipitated by adding 700 l of isopropanol inverting to mix, centrifuging for 10 minutes 10,000rpm at 4˚C. Isopropanol was removed, and DNA pellet washed twice with 70% ethanol, dried, and resuspended in 100 l of dH2O. DNA integrity was validating by running on an agarose gel and concentration quantified by qubit and sequenced by MIGS or SeqCoast where libraires were generated using the Illumina DNA Prep kit and custom IDT 10bp unique dual indices (UDI) with a target insert size of 320 bp. Sequencing was performed on an Illumina NovaSeq 6000 sequencer in one or more multiplexed shared-flow-cell runs, producing 2x151bp paired-end reads.
characteristics.characteristic: description
characteristics.text: Smooth
characteristics.characteristic: encoded_traits
characteristics.text: Human
characteristics.characteristic: env_broad_scale
characteristics.text: not applicable
characteristics.characteristic: env_local_scale
characteristics.text: 7H9 +Tryptone
characteristics.characteristic: env_medium
characteristics.text: USA: Altanta
characteristics.characteristic: geo_loc_name
characteristics.text: Homo sapiens
characteristics.characteristic: host
characteristics.text: Cystic Fibrosis
characteristics.characteristic: host_disease
characteristics.text: not applicable
characteristics.characteristic: isol_growth_condt
characteristics.text: CF Sputum
characteristics.characteristic: isolation_source
characteristics.text: not applicable
characteristics.characteristic: lat_lon
characteristics.text: not applicable
characteristics.characteristic: num_replicons
characteristics.text: Mycobacteroides abscessus subsp. abscessus
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/NCBITaxon_1185650
characteristics.characteristic: organism
characteristics.text: not applicable
characteristics.characteristic: ref_biomaterial
characteristics.text: EN37
characteristics.characteristic: strain
characteristics.text: abscessus
characteristics.characteristic: sub_species
characteristics.text: EN37
characteristics.characteristic: title