|
| Status |
Public on Jul 25, 2022 |
| Title |
murine kidney_non-infected_7day_biological rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Kidney from mice inoculated with sterile EMJH medium after 7 days
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
genotype: WT
gender: Female
age: 6-8 weeks
tissue: Kidney
infection: None
|
| Treatment protocol |
Bacteria were propagated at 28 °C under aerobic conditions in medium containing 10% Leptospira enrichment Elinghausen-McCullough-Johnson-Harris (EMJH) medium (BD Diagnostics) and 90% Leptospira medium base EMJM medium (Difco, Sparks, MD). The number of motile leptospires was counted using dark-field microscopy and a Petroff-Hausser counting chamber for experimental infections. Mice were inoculated using intraperitoneal challenge with 10^9 Leptospira spp. in 0.1 ml EMJH medium and the control groups were inoculated with sterile EMJH medium.
|
| Growth protocol |
C57BL/6 female mice aged 6–8 weeks were used for this study. All animal experiments were handled under Animal Biosafety Level 2 conditions and followed all appropriate guidelines for the use of infected animals.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from kidney tissues using the TRIzol reagent (Invitrogen, Carlsbad, CA) with DNaseI digestion. The quantity and integrity of extracted RNA were verified using a Nano-Drop spectrophotometer (Thermo Fisher Scientific, Waltham, MA) and an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA).
Total RNA samples were converted to cDNA using the Ovation RNA-seq System V2 (NuGEN). Library construction was performed using the Ovation Ultralow Library System V2 1-96 (NuGEN).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
E423
Expression data from non-infected mice kidney tissue.
Sterilized Ellinghausen-McCullough-Johnson-Harris (EMJH) medium.
After inoculation at day 7
|
| Data processing |
Primary sequencing data was produced by Illumina Hiseq 2000 and 4000 Sequencing System (Flowcell ID: 0416 and HL2F3BBXX).
Fastq files are quality checked with FastQC, v0.11.5 (Babraham Bioinformatics, Cambridge, UK).
Sequenced reads were trimmed using the CLC Genomics Workbench V9.5 on the basis of the per base sequence quality score (Q) >= 20.
After this trimming step, sequenced reads were mapped to Mus_musculus GRCM38 using the CLC Genomics Workbench V9.5.
RPKM, Reads Per Kilobase of exon model per Million mapped reads, values for estimating transcript expression levels were done using the CLC Genomics Workbench V9.5.
Genome_build: Mus_musculus GRCm38
Supplementary_files_format_and_content: Tab-delimited text files contain gene name, ID, reads and RPKM values.
|
| |
|
| Submission date |
Oct 05, 2021 |
| Last update date |
Jul 25, 2022 |
| Contact name |
Li-Fang Chou |
| E-mail(s) |
d928209@gmail.com
|
| Phone |
+886-3-3281200
|
| Organization name |
Chang Gung Memorial Hospital, Linkou
|
| Department |
Department of Medical Research and Development
|
| Lab |
Kidney Research Center
|
| Street address |
5 Fu-Shing St., Kueishan
|
| City |
Taoyuan |
| ZIP/Postal code |
333 |
| Country |
Taiwan |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE185382 |
High-throughput renal transcriptome profiling in mice infected with Leptospira spp. |
|
| Relations |
| BioSample |
SAMN22067160 |
| SRA |
SRX12493244 |
