|
Status |
Public on Mar 03, 2023 |
Title |
platelet baseline WT rep1 |
Sample type |
SRA |
|
|
Source name |
platelet
|
Organism |
Mus musculus |
Characteristics |
cell type: platelet genotype: WT condition: baseline
|
Extracted molecule |
total RNA |
Extraction protocol |
purification of platelets was performed using immune-magnetic negative selection to completely deplete leukocytes. Total RNA including miRNA was isolated from murine platelets using the QIAsymphony RNA Kit. The sequencing library was prepared using the QIAseq miRNA Library Kit with 10 to 20 ng input. The libraries were pooled in an equimolar fashion and sequenced on a NovaSeq6000 as paired-end reads with a sequencing depth of >12 Mio clusters (i.e. read-pairs) per sample.
|
|
|
Library strategy |
miRNA-Seq |
Library source |
transcriptomic |
Library selection |
size fractionation |
Instrument model |
Illumina NovaSeq 6000 |
|
|
Data processing |
FastQC (version 0.11.8) adapter were trimmed using Trim Galore! (version 0.6.3) Alignment against miRBase mature and hairpin was performed using Bowtie (version1.3.0) Ensembl annotations miRBase mature and miRbase from the GRCm38 Post-alignment processing of miRBase hairpin was performed using SAMtools (version 1.10.2) Analysis of miRBase counts was performed using edgeR (version 3.11) and TMM normalization miRNA quality control was validated using mirtrace (version 1.0.0) Genome_build: GRCm38 Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample, matrix table with raw gene counts for every gene and every sample
|
|
|
Submission date |
Sep 21, 2021 |
Last update date |
Mar 03, 2023 |
Contact name |
Oliver Borst |
Organization name |
University Clinic Tübingen
|
Department |
Internal Medicine III- Cardiology
|
Lab |
AG Borst
|
Street address |
Otfried-Müller-Street 10
|
City |
Tübingen |
ZIP/Postal code |
72076 |
Country |
Germany |
|
|
Platform ID |
GPL24247 |
Series (1) |
GSE184523 |
Murine platelet miRNA pattern and its regulation by a MK/platelet-specific genetic ablation of Dicer. |
|
Relations |
BioSample |
SAMN21533486 |
SRA |
SRX12281036 |