|
|
GEO help: Mouse over screen elements for information. |
|
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 Selector |
Raw data are available in SRA |
|
|
|
|
|