Model organism or animal
BioSampleModel
2022-07-06
ENA-FIRST-PUBLIC
2022-07-06
ENA-LAST-UPDATE
SAMN25028012
External Id
pda|tdoniger
INSDC center alias
pda|tdoniger
INSDC center name
2022-07-06T11:24:54Z
INSDC first public
2022-07-06T11:24:54Z
INSDC last update
public
INSDC status
SRS11690491
SRA accession
PCF PRS -CMC TGIRT
Submitter Id
NCBI
broker name
Procyclic form
cell_line
Procyclic form
cell_subtype
Procyclic form
cell_type
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 TGIRTTM-III Enzyme (InGex). The RNA was subsequently degraded using 2 ml 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).
description
Procyclic form
dev_stage
Procyclic T. brucei 427 wild-type strain and the genetically modified 29–13 strains, which carries integrated genes for T7 polymerase and the tetracycline repressor, were grown in SDM-79 medium supplemented with 10% fetal calf serum.
growth_protocol
Procyclic T. brucei 427 wild-type strain
isolate
Post ribosomal supernatant (PRS)
isolation_source
Trypanosoma brucei
http://purl.obolibrary.org/obo/NCBITaxon_5691
organism
Post ribosomal supernatant (PRS)
sample_type
not applicable
sex
not applicable
tissue
Trypanosoma brucei
title
RNA was subjected to alkali hydrolysis with Na2CO3 (50 mM, pH 10. 4) at 37oC for 4h. The reacted RNA was recovered by phenol: chloroform extraction, and ethanol precipitation.
treatment