|
| Status |
Public on Apr 01, 2024 |
| Title |
MybM_OE_30hrs_Shield_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: Shield-1 (0.5 µM) 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 |
| E-mail(s) |
kwalzer@vet.upenn.edu
|
| 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 |
|
| Relations |
| BioSample |
SAMN40569736 |
| SRA |
SRX24017308 |
