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Sample GSM8159266 Query DataSets for GSM8159266
Status Public on Apr 01, 2024
Title MybM_OE_30hrs_vehicle_rep_3
Sample type SRA
Source name HCT-8
Organism Cryptosporidium parvum
Characteristics source: Cryptosporidium parvum infected HCT-8 cells
background strain: Cryptosporidium parvum Iowa II (Bunchgrass Farms)
genotype: cgd6_2250 (Myb-M) OE in TK locus
treatment: vehicle (0.1% ethanol) for 6 hours
cell preparation: bulk
cell type: HCT-8
Treatment protocol Cultures were treated with vehicle (0.1% ethanol) or Shield-1 (0.5 µM) for 6 hours starting at 24 hours (three biological replicates per strain and condition)
Growth protocol HCT-8 cells grown in a 24-well plate were infected with 250,000 oocysts of wild-type or Myb-M-HA overexpression parasites for 30 hours at 5% CO2 and 37º C
Extracted molecule total RNA
Extraction protocol RNA was isolated using the RNeasy Mini Kit (Qiagen) and processed as per manufacturer’s instructions
Libraries were prepared using the Illumina stranded mRNA prep ligation kit (20040534), according to the manufacturer’s instructions
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model NextSeq 2000
Description RNeasy minikit, Illumina stranded mRNA prep ligation kit (20040534)
Data processing Fastq files were pseudoaligned to the Cryptosporidium parvum Iowa II reference transcriptome (version 46, VEuPathDB) using Kallisto v.0.45.0
Kallisto transcript counts were imported into R using the Bioconductor package tximport
Expression data was normalized using the TMM method in the function calcNormFactors from the package edgeR
Differentially expressed genes (log2 fold-change ≥ 1 and p-value ≤ 0.05) were identified by linear modeling and Bayesian statistics using the limma package
Assembly: Version 46 of the Cryptosporidium parvum Iowa II reference from VEuPathDB
Supplementary files format and content: Tab-delimited text files include log2 counts per million (CPM) values for each sample
Submission date Mar 21, 2024
Last update date Apr 01, 2024
Contact name Katelyn Ann Walzer
Organization name University of Pennsylvania
Department Pathobiology
Lab Striepen
Street address 380 South University Avenue
City Philadelphia
State/province PA
ZIP/Postal code 19104
Country USA
Platform ID GPL34324
Series (1)
GSE232438 Transcriptional control of the Cryptosporidium lifecycle
BioSample SAMN40569739
SRA SRX24017305

Supplementary data files not provided
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Raw data are available in SRA

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