|
| Status |
Public on Oct 02, 2023 |
| Title |
C. parvum-infected cells, replicate 3 [cp_24_R3_T1] |
| Sample type |
SRA |
| |
|
| Source name |
Primary intestinal stem cells, differentiated
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: Primary intestinal stem cells, differentiated
cell type: epithelial intestinal cells (hALI)
genotype: WT
treatment: C. parvum-infected cells
time: H24
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were homogenized using a QiaShredder column (QIAGEN) and total RNA was purified using an RNeasy Mini kit (QIAGEN), then RNA libraries were prepared using standard Illumina techniques
Samples were prepared according to library kit manufacturer’s protocol, indexed, pooled, and sequenced on an Illumina NovaSeq 6000.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Raw reads from fastq files were mapped to the human reference transcriptome (Ensembl; Homo sapiens version 86) using Kallisto, version 0.46.0. All subsequent analyses were carried out using the statistical computing environment, R version 4.0.4 in RStudio version 2022.07.2 and Bioconductor, version 3.12
Transcript-level counts and abundance data were imported into R and summarized to gene level using the TxImport package. Data was normalized using the TMM method in EdgeR. Differentially expressed genes (FC>2 and FDR<.05) were identified on filtered-normalized, not batch-corrected gene expression matrix by linear modeling and Bayesian statistics using the Limma packageon.
Assembly: Ensembl; Homo sapiens version 86, GRCh38 Release 97
Supplementary files format and content: Tab-delimited text raw data includes raw gene counts summarized by tximport package
Supplementary files format and content: Filtered and normalized data file format and content: Tab-delimited text filtered normalized data includes gene expression for each sample after normalization with EdgeR package (TMM method).
Supplementary files format and content: Study design: Comma-separated values file with study design
|
| |
|
| Submission date |
Aug 23, 2023 |
| Last update date |
Oct 02, 2023 |
| Contact name |
L. David Sibley |
| E-mail(s) |
sibley@wustl.edu
|
| Organization name |
Washington University School of Medicine
|
| Department |
Molecular Microbiology
|
| Street address |
425 S. Euclid Ave
|
| City |
St. Louis |
| State/province |
MO |
| ZIP/Postal code |
63110-1093 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE241571 |
Cryptosporidium infection of human small intestinal epithelial cells induces type III interferon expression and impairs the infectivity of live-attenuated rotavirus vaccines [hALI_Cp] |
| GSE241572 |
Cryptosporidium infection of human small intestinal epithelial cells induces type III interferon expression and impairs the infectivity of live-attenuated rotavirus vaccines. |
|
| Relations |
| BioSample |
SAMN37128074 |
| SRA |
SRX21472216 |
