|
| Status |
Public on Sep 30, 2022 |
| Title |
3B_S16_R1_001 (paired) |
| Sample type |
SRA |
| |
|
| Source name |
Skin
|
| Organisms |
Streptococcus agalactiae; Mus musculus |
| Characteristics |
tissue: Skin
treatment: Diabetic infected
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using Rneasy mini plus kit (Qiagen).RNA was extracted from 2-3 mice before pooling RNA to form triplicate samples. For bacteria, we utilized three input controls as replicates and again pooled from 2-3 mice for all bacterial samples.
Samples were rRNA depleted using RiboZero Plus (Illumina) and libraries for the 12 mouse samples and 3 input bacteria cDNA samples were sequenced using the Illumina Stranded RNA sequencing platform.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
CLC Genomics Workbench v 21.0.5
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Reads were aligned to the rRNA track of CP063198_sRNA and unmapped reads used for RNA-seq
Trimmed sequence reads were mapped first to mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Unmapped sequence reads were then mapped to CP063198_sRNA using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: CP063198_sRNA
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample
|
| |
|
| Submission date |
Apr 22, 2022 |
| Last update date |
Sep 30, 2022 |
| Contact name |
Kelly Doran |
| E-mail(s) |
[email protected], [email protected]
|
| Phone |
3037243539
|
| Organization name |
University of Colorado Anschutz Medical Campus
|
| Department |
Immunology and Microbiology
|
| Street address |
12800 E 19th Ave
|
| City |
Aurora |
| State/province |
Colorado |
| ZIP/Postal code |
80045 |
| Country |
USA |
| |
|
| Platform ID |
GPL32195 |
| Series (1) |
| GSE201342 |
Group B Streptococcal Pathogenesis in Diabetic Wounds |
|
| Relations |
| BioSample |
SAMN27740728 |
| SRA |
SRX14972176 |
