characteristics.text: SAMN26497764
characteristics.characteristic: External Id
characteristics.text: Bar Ilan University
characteristics.characteristic: INSDC center name
characteristics.text: 2024-05-09T00:00:00Z
characteristics.characteristic: INSDC first public
characteristics.text: 2024-05-09T08:39:01.849Z
characteristics.characteristic: INSDC last update
characteristics.text: SRS13738920
characteristics.characteristic: INSDC secondary accession
characteristics.text: live
characteristics.characteristic: INSDC status
characteristics.text: Model organism or animal
characteristics.characteristic: NCBI submission model
characteristics.text: Model.organism.animal.1.0
characteristics.characteristic: NCBI submission package
characteristics.text: SRS13738920
characteristics.characteristic: SRA accession
characteristics.text: To perform HydraPsiSeq, the fragmented RNA (~800ng) was dephosphorylated with FastAP Thermosensitive Alkaline Phosphatase (Thermo Scientific), cleaned by Agencourt RNA clean XP beads (Beckman Coulter) and ligated to a 3’ linker using high concentration T4 RNA Ligase 1 (NEB) in a buffer containing DMSO, ATP, PEG 8000, and RNase inhibitor (NEB). The ligated RNA was cleaned from excess linker using Dynabeads® MyOne™ SILANE beads (Thermo Scientific), and first strand cDNA was prepared using the AffinityScript Reverse Transcriptase enzyme (Agilent). The RNA was subsequently degraded using 2l of 1 M NaOH, and the cDNA was cleaned using Dynabeads® MyOne™ SILANE beads (Thermo Scientific). The cDNA was further ligated to a 3’ adapter using high concentration T4 RNA Ligase 1 (NEB) and cleaned of excess adapter by using Dynabeads® MyOne™ SILANE beads (Thermo Scientific). The adapter ligated cDNA was PCR enriched using NEBNext® High-Fidelity (NEB) polymerase (9 PCR cycles), separated on an E-Gel EX agarose gel (Invitrogen) and size selected in the range of 150-300 bp (containing ~30-180 nt corresponding to RNA). The amplicons were gel purified using NucleoSpin Gel and PCR Clean-up kit (Macherey-Nagel), and sequenced in a Nextseq system (Illumina) in paired end mode (20 million reads for each sample).
characteristics.characteristic: description
characteristics.text: Amastigote
characteristics.characteristic: dev_stage
characteristics.text: mCherry transgenic, tissue-derived amastigotes of Leishmania amazonensis strain LV79 (WHO reference number MPRO/BR/72/M1841) were isolated from infected footpads of Swiss nude mice.
characteristics.characteristic: growth_protocol
characteristics.text: mCherry transgenic, tissue-derived amastigotes of Leishmania amazonensis strain LV79 (WHO reference number MPRO/BR/72/M1841) were isolated from infected footpads of Swiss nude mice.
characteristics.characteristic: isolate
characteristics.text: Leishmania amazonensis
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/NCBITaxon_5659
characteristics.characteristic: organism
characteristics.text: Total RNA
characteristics.characteristic: sample_type
characteristics.text: not applicable
characteristics.characteristic: sex
characteristics.text: LV79(MPRO/BR/72/M1841)
characteristics.characteristic: strain
characteristics.text: not applicable
characteristics.characteristic: tissue
characteristics.text: Model organism or animal sample from Leishmania amazonensis
characteristics.characteristic: title
characteristics.text: Hydrazine 45'- aniline 15'
characteristics.characteristic: treatment