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Sample GSM5543502 Query DataSets for GSM5543502
Status Public on Jan 07, 2022
Title TbPOLIE RNAi uninduced (-D) rep 1
Sample type SRA
 
Source name culcured cells
Organism Trypanosoma brucei brucei
Characteristics strain: lister 427
genotype/variation: TbPOLIE+Myc/+ RNAi
genotype/variation: TbPOLIE-myc (endogenous tagging)
treatment: -doxycycline
Treatment protocol 100 ng/ml doxycycline (to induce TbPOLIE RNAi) for 30 hrs
Growth protocol Bloodstream T. brucei cells were cultured in HMI9 medium with 10% FBS. All cells were maintained with medium containing 2 µg/ml G418, 4 µg/ml Hygromycin, and 2 µg/ml of Phleomycin.
Extracted molecule polyA RNA
Extraction protocol Total RNA was isolated and purified through RNeasy columns (Qiagen). RNA samples were run on a BioAnalyzer 2100 (Agilent Technologies) using the Agilent RNA 6000 nano kit to verify the RNA quality before sent to Novogene, where RNA degradation and contamination were monitored on 1% agarose gels. RNA purity was checked using the NanoPhotometer® spectrophotometer (IMPLEN). RNA integrity and quantitation were assessed using the RNA Nano 6000 Assay Kit on a Bioanalyzer 2100 system (Agilent Technologies).
Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) using 1 μg poly(A) RNA according to manufacturer’s protocol and index codes were added to attribute sequences to each sample.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Data processing Base-calling using NovaSeq 6000 for Illumina sequencing
Raw reads were first processed with Novogene Perl Scripts (removing reads with low quality, with adapters, and containing poly-N; calculating Q20, Q30 and GC contents).
Clean reads were mapped to T. brucei Lister 427 genome TriTrypDB-45_TbruceiLister427_2018_Genome.fasta and its annotation TriTrypDB-45_TbruceiLister427_2018.gff Idownloaded from the TriTryp DB) using HISAT2.
HTSeq v0.6.1 was used to count the read numbers mapped to each gene. FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene
Differential expression analysis of two conditions/groups (three biological replicates per condition) was performed using the DESeq R package (1.18.0)
 
Submission date Aug 27, 2021
Last update date Jan 07, 2022
Contact name Bibo Li
E-mail(s) b.li37@csuohio.edu
Phone 216 6872444
Organization name CLEVELAND STATE University
Department Center for Gene Regulation in Health and Disease
Street address 2121 Euclid Avenue
City CLEVELAND
State/province OH
ZIP/Postal code 44115
Country USA
 
Platform ID GPL27986
Series (1)
GSE182941 POLIE suppresses telomerase-mediated telomere G-strand extension and helps ensure proper telomere C-strand synthesis in trypanosomes
Relations
BioSample SAMN21024289
SRA SRX11952362

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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