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Sample GSM8482193 Query DataSets for GSM8482193
Status Public on Aug 31, 2024
Title PCF_wt_2
Sample type SRA
 
Source name Lister 427
Organism Trypanosoma brucei
Characteristics strain: Lister 427
genotype: PCF
treatment: wt
Treatment protocol T. brucei parasites in logarithmic phase were incubated with 2X of the half-maximal inhibitory concentration of AQ1 (BSF: 0,24 uM and PCF: 9), Pt-TTPY (BSF: 0,26 uM and PCF: 48,46 uM) and pyridostatin (BSF: 11,04 uM and PCF: 18,18 uM) for 18 h at 37ºC or 28 ºC, 5% CO2 and 100% of humidity
Growth protocol Bloodstream forms of T. brucei brucei “single marker” S427 (S16) (Lister 427, antigenic type MiTat 1.2, clone 221a) were grown at 37 °C, 5% CO2 in HMI-9 medium supplemented with 10% heat-inactivated fetal bovine serum (Invitrogen, EEUU); Procyclic forms of T. brucei 449 were cultured at 28°C, 5% CO2 in SDM-79 medium containing 10% hiFBS (Invitrogen, EEUU) and 7.5 μg ml−1 hemin (Sigma-Aldrich, EEUU).
Extracted molecule total RNA
Extraction protocol Total RNA was purified using a total RNA isolation kit (Qiagen, Germany)
NEBNext® Ultra™ II DNA Library Prep Kit for Illumina
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model NextSeq 1000
 
Data processing Reads were mapped with STAR v2.7.10b
Featurecounts were done with FeatureCounts from the package Subread v2.0.4
Assembly: TriTrypDB-63_TbruceiLister427_2018 from https://tritrypdb.org/
Supplementary files format and content: Tab delimited tables with Read Count data
 
Submission date Aug 26, 2024
Last update date Aug 31, 2024
Contact name Anne de Jong
E-mail(s) anne.de.jong@rug.nl
Phone +31 50 363 2047
Organization name university of Groningen
Department Molecular Genetics
Street address Nijenborgh 7
City Groningen
ZIP/Postal code 9747 AG
Country Netherlands
 
Platform ID GPL34844
Series (1)
GSE275674 Insight into the epigenetic regulation of gene expression in the bloodstream and procyclic forms of Trypanosoma brucei through the involvement of G-Quadruplexes
Relations
BioSample SAMN43370120
SRA SRX25830918

Supplementary file Size Download File type/resource
GSM8482193_PCF_wt_2.1.counts.gz 395.2 Kb (ftp)(http) COUNTS
SRA Run SelectorHelp
Raw data are available in SRA

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