|
| Status |
Public on Jul 10, 2024 |
| Title |
Cryptosporidium parvum, ileum, adult, rep1 |
| Sample type |
SRA |
| |
|
| Source name |
C. parvum parasites
|
| Organism |
Cryptosporidium parvum |
| Characteristics |
cell type: C. parvum parasites
genotype: C. parvum INRAE Nluc
digestive compartment: Ileal effluents
time: 120-180 min
age condition: Adult
|
| Treatment protocol |
Child or adult digestion in the dynamic TIM-1 in vitro gastrointestinal model
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extracted using Direct-zol RNA Microprep kit (Zymo Research), Dnase I-treated using Dnase I Set kit (Zymo Research) and further purified using RNA Clean & Concentrator-5 kit (Zymo Research)
RNA libraries were prepared using QuantSeq 3' mRNA-Seq Library Prep kit FWD for Illumina (Lexogen)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Ileal_120-180_4
|
| Data processing |
Raw sequence data were assessed for quality using the FastQC v0.11.3 tool
Sequenced reads were aligned to the C. parvum IOWA-ATCC reference genome (assembly ASM1524537v1) using the STAR software
Gene counts were determined using the STAR software
R-based packages DESeq2 and edgeR were used to normalise data
Assembly: NCBI Genome assembly ASM1524537v1
Supplementary files format and content: Tab-delimited text file including raw counts for all samples
|
| |
|
| Submission date |
Jul 01, 2024 |
| Last update date |
Jul 10, 2024 |
| Contact name |
Julie TOTTEY |
| E-mail(s) |
julie.tottey@inrae.fr
|
| Organization name |
INRAE
|
| Street address |
INRAE Val de Loire UMR ISP 1282
|
| City |
NOUZILLY |
| ZIP/Postal code |
37380 |
| Country |
France |
| |
|
| Platform ID |
GPL26382 |
| Series (1) |
| GSE271211 |
Effect of human child or adult digestion reproduced in a dynamic in vitro gastrointestinal model on Cryptosporidium parvum transcriptome |
|
| Relations |
| BioSample |
SAMN42206201 |
| SRA |
SRX25168282 |
