characteristics.text: SAMN26497770
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: 2024-05-09T08:39:02.023Z
characteristics.characteristic: INSDC last update
characteristics.text: SRS13738930
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: SRS13738930
characteristics.characteristic: SRA accession
characteristics.text: To perform Ψ-seq, the CMC treated and un-treated total RNA (~800 ng) was fragmented and 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) and sequenced in a Nextseq system (Illumina) in paired end mode (40 million reads for each sample).
characteristics.characteristic: description
characteristics.text: Promastigote
characteristics.characteristic: dev_stage
characteristics.text: Leishmania donovani strain 1S2D (MHOM/SD/62/1S-CL2D) was maintained by serial passages in hamsters. Amastigotes were recovered from infected hamster spleen and differentiated into promastigotes in M199 complete medium (M199, 10% FBS, 20 mM HEPES; 100 µM adenine, 2 mM L-glutamine, 10 µg/ml folic acid, 13.7 µM hemin, 4.2 mM NaHCO3, 1xRPMI1640 vitamins, 8 µM 6-biopterin, 100 units penicillin and 100 µg/ml streptomycin, pH 7.4) at 26°C.
characteristics.characteristic: growth_protocol
characteristics.text: Leishmania donovani strain 1S2D (MHOM/SD/62/1S-CL2D) was maintained by serial passages in hamsters. Amastigotes were recovered from infected hamster spleen and differentiated into promastigotes in M199 complete medium..
characteristics.characteristic: isolate
characteristics.text: Leishmania donovani
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/NCBITaxon_5661
characteristics.characteristic: organism
characteristics.text: Total RNA
characteristics.characteristic: sample_type
characteristics.text: not applicable
characteristics.characteristic: sex
characteristics.text: 1S2D (MHOM/SD/62/1S-CL2D)
characteristics.characteristic: strain
characteristics.text: not applicable
characteristics.characteristic: tissue
characteristics.text: Model organism or animal sample from Leishmania donovani
characteristics.characteristic: title
characteristics.text: CMC minus
characteristics.characteristic: treatment