|
| Status |
Public on Jan 08, 2024 |
| Title |
IL1b d6 #1 |
| Sample type |
SRA |
| |
|
| Source name |
Colon
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Colon
genotype: IL1bKO
treatment: Salmonella infection
|
| Treatment protocol |
WT and IL-1b-/- C57BL/6 mice were orally infected with 10^7 CFU of Salmonella typhimurium SL1334. Colonic tissues were removed at 2 and 6 days post infection and RNA was exptracted and sequenced.
|
| Growth protocol |
Mice grown under SPF conditions
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA from frozen colonic tissues was extracted using Qiagen RNeasy Universal kit. Integrity of the isolated RNA was analysed using the Agilent TS HS RNA Kit and TapeStation 4200
1000ng of total RNA was treated with the NEBNext poly (A) mRNA Magnetic Isolation Module (NEB, #E7490L). RNA sequencing libraries were produced by using the NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB #E7770L). Quantification of the library was performed using a dsDNA HS Assay Kit and Qubit (Molecular Probes, Life Technologies) and qualification was done using the Agilent TS D1000 kit and TapeStation 4200. 250nM of each library was pooled together and diluted to 4nM according to the NextSeq manufacturer’s instructions. 1.6pM was loaded onto the Flow Cell with 1% PhiX library control. Libraries were sequenced with the Illumina NextSeq 550 platform with single-end reads of 75 cycles according to the manufacturer's instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
| |
|
| Description |
S22
|
| Data processing |
Sequencing data was trimmed, aligned and normalized (reads per million mapped reads) using default settings via Partek bioinformatics software.
Assembly: GRCm38
Supplementary files format and content: Xlsx file includes RPKM values for each Sample
|
| |
|
| Submission date |
Dec 26, 2023 |
| Last update date |
Jan 08, 2024 |
| Contact name |
Shai Bel |
| E-mail(s) |
shai.bel@biu.ac.il
|
| Organization name |
Bar-Ilan University
|
| Department |
The Azrieli Faculty of Medicine
|
| Street address |
8 Henrietta Szold St, P.O. Box 1589
|
| City |
Safed |
| ZIP/Postal code |
1311502 |
| Country |
Israel |
| |
|
| Platform ID |
GPL21626 |
| Series (2) |
| GSE252069 |
Salmonella manipulates the host to drive pathogenicity via induction of interleukin 1β [RNA-Seq] |
| GSE252071 |
Salmonella manipulates the host to drive pathogenicity via induction of interleukin 1β |
|
| Relations |
| BioSample |
SAMN39127985 |
| SRA |
SRX23029001 |
