|
| Status |
Public on Apr 14, 2021 |
| Title |
Tregs_1-45_1 |
| Sample type |
SRA |
| |
|
| Source name |
brochoalveolar lavage of mice
|
| Organism |
Mus musculus |
| Characteristics |
tissue: lung
cell type: regulatory t cells without bound platelets
treatment: 5 days after induction of bacterial pneumonia
|
| Treatment protocol |
Bacterial pneumonia was induced in wildtype mice by intratracheal instillation of viable bacteria (K. pneumonia). Cells were isolated from BAL on day 5 after induction of bacterial pneumonia.
|
| Growth protocol |
N/A
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from the sorted cells using a RNeasy Mini Kit (Qiagen).
Reverse transcription into cDNA was performed based on polyA tail. For library construction, PCR products were purified and selected with the Agencourt AMPure XP-Medium kit. The single strand circle DNA (ssCirDNA) were formatted as the final library. The library was amplified to make DNA nanoball (DNB) which had more than 300 copies of one molecular. The DNBs were loaded into the patterned nanoarray and single end 50 bases reads were generated in the way of sequenced by combinatorial Probe-Anchor Synthesis (cPAS).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
BGISEQ-500 |
| |
|
| Data processing |
quality control was performed with FastQC and MultiQC and adapter trimming was performed with trim-galore (v0.6.4).
Read-mapping and quantification with Salmon (v1.0.0) using the Gencode mouse reference transcriptome vM23
The transcript counts where summarized to gene-level with tximport and supplementary annotation data from Ensembl
The differential expression analysis was carried out by DESeq2 on gene level counts
The reported log foldchanges where shrunk with apeglm and s-values where calculated for statistical significance filtering. For a significant differential gene we require a s-value below 0.01.
Genome_build: mm10
Supplementary_files_format_and_content: Tab separated matrix of quantification counts of each gene per sample.
|
| |
|
| Submission date |
Apr 13, 2021 |
| Last update date |
Apr 14, 2021 |
| Contact name |
Jan Rossaint |
| E-mail(s) |
jan@rossaint.net
|
| Organization name |
University of Münster
|
| Department |
Dpt. of Anesthesiology
|
| Street address |
Albert-Schweitzer-Campus 1, Bldg. A1
|
| City |
Münster |
| ZIP/Postal code |
48149 |
| Country |
Germany |
| |
|
| Platform ID |
GPL23479 |
| Series (1) |
| GSE171989 |
Platelets orchestrate the resolution of pulmonary inflammation in mice through Treg repositioning and macrophage education |
|
| Relations |
| BioSample |
SAMN18723888 |
| SRA |
SRX10593130 |
