|
| Status |
Public on Jan 15, 2018 |
| Title |
5 dpi YPIII deltacnfY-2 |
| Sample type |
SRA |
| |
|
| Source name |
infected cecal tissue
|
| Organism |
Mus musculus |
| Characteristics |
tissue: cecal tissue
strain: Balb/c, Yersinia pseudotuberculosis
age: 6-10 weeks
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from homogenized and tissue lysed cecal tissue using phenol extraction.
Purification of mRNA was done using human/mouse/rat ScriptSeq complete kit (Illumina). Following the purification, the RNA was used for library preparation using Script Seq v2 Library preparation kit (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
+ cnfY mutant bactera, cecal tissue
|
| Data processing |
library quality assessment using FastQC
alignment vs. reference genome using Tophat2 (V1.20) with default parametrization
read count quantification using htseq-count (http://www.huber.embl.de/users/anders/HTSeq)
Detection of differentially expressed genes using DeSEQ2 with raw count data and default parametrization. Cook distance cutoff filter disabled
Genome_build: Mus musculus GRCm38
Supplementary_files_format_and_content: htseqcounts*.tab files: CSV format with raw read counts per gene; des2rlog*.tab files: CSV format with DESeq2 rlog transformed read counts per gene; DESeq2_genes_diffexp*.csv: CSV files with differentially expressed genes
|
| |
|
| Submission date |
May 11, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Michael Beckstette |
| Organization name |
Helmholtz Centre for Infection Research
|
| Department |
Molecular Infection Biology
|
| Lab |
Experimental Immunology
|
| Street address |
Inhoffenstrase 7
|
| City |
Braunschweig |
| State/province |
Lower Saxony |
| ZIP/Postal code |
38124 |
| Country |
Germany |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE98802 |
Loss of CNFy toxin-induced inflammation drives Yersinia pseudotuberculosis into persistency |
|
| Relations |
| BioSample |
SAMN06928692 |
| SRA |
SRX2796956 |
