|
| Status |
Public on Nov 24, 2023 |
| Title |
WT_CVB3_6d_3 |
| Sample type |
SRA |
| |
|
| Source name |
Heart
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Heart
genotype: wildtype
treatment: CVB3
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA Isolation was performed using the miRNeasy mini kit (Qiagen, Germany). As suggested, DNase I (Qiagen, Germany) was applied to the column to avoid genomic DNA contamination.
Three prime End sequencing using GenXPro-MACE-Seq kit (GenXPro GmbH, Frankfurt Germany) including UMIs for PCR-dupliacate removal.
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Sample 9
|
| Data processing |
Illumina bcl2fastq software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and bad quality as well as MACE specific polyA stretches; PCR artifacts were deduplicated based on Unique Molecular Identifier sequences
Cleaned reads were mapped onto mm10 genome using bowtie2 and raw counts were obtained using HTSeq
Differential gene expression was calculated using DESeq2.
Assembly: mm10
Supplementary files format and content: raw count and tpm count
Library strategy: Massive Analysis of cDNA ends (MACE-Seq)
|
| |
|
| Submission date |
Nov 23, 2023 |
| Last update date |
Nov 24, 2023 |
| Contact name |
Diana Lindner |
| E-mail(s) |
diana.lindner@uniklinik-freiburg.de
|
| Organization name |
University Hospital Freiburg
|
| Department |
University Heart Center Freiburg-Bad Krozingen
|
| Street address |
Hugstetter Straße 55
|
| City |
Freiburg |
| ZIP/Postal code |
79106 |
| Country |
Germany |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE248521 |
GPR15-mediated T cell recruitment during acute viral myocarditis facilitated virus elimination and improved outcome |
|
| Relations |
| BioSample |
SAMN38391717 |
| SRA |
SRX22629151 |
