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| Status |
Public on Aug 31, 2024 |
| Title |
AJ_BSF_wt_1 |
| Sample type |
SRA |
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| Source name |
Lister 427
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| Organism |
Trypanosoma brucei |
| Characteristics |
genotype: BCF
treatment: wt
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| 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
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| 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).
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| 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
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 1000 |
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| 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
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| Submission date |
Aug 26, 2024 |
| Last update date |
Sep 04, 2024 |
| Contact name |
Anne de Jong |
| E-mail(s) |
anne.de.jong@rug.nl
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| Phone |
+31 50 363 2047
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| Organization name |
university of Groningen
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| Department |
Molecular Genetics
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| Street address |
Nijenborgh 7
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| City |
Groningen |
| ZIP/Postal code |
9747 AG |
| Country |
Netherlands |
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| 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 |
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| Relations |
| BioSample |
SAMN43370113 |
| SRA |
SRX25830925 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8482200_AJ_BSF_wt_1.1.counts.gz |
396.8 Kb |
(ftp)(http) |
COUNTS |
SRA Run Selector |
| Raw data are available in SRA |
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