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Sample GSM5591888 Query DataSets for GSM5591888
Status Public on Mar 03, 2023
Title platelet baseline KO rep4
Sample type SRA
 
Source name platelet
Organism Mus musculus
Characteristics cell type: platelet
genotype: KO
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 SAMN21533493
SRA SRX12281043

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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