Model organism or animal
BioSampleModel
2022-07-06
ENA-FIRST-PUBLIC
2022-07-06
ENA-LAST-UPDATE
SAMN25028014
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
SRS11690493
SRA accession
BSF PRS -CMC TGIRT
Submitter Id
NCBI
broker name
Bloodstream form
cell_line
Bloodstream form
cell_subtype
Bloodstream 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
Bloodstream form
dev_stage
T. brucei 427 BSF wild-type cells was aerobically cultivated at 37°C under 5% CO2 in HMI-9 medium supplemented with 10% fetal calf serum.
growth_protocol
T. brucei 427 BSF wild-type
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