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Sample GSM4708655 Query DataSets for GSM4708655
Status Public on Dec 21, 2021
Title Platelets from Pf4Cre-Srsf3fl/fl mice, replicate 3
Sample type SRA
 
Source name Platelets
Organism Mus musculus
Characteristics strain: C57BL/15
tissue: Platelets
genotype: Pf4Cre-Srsf3fl/fl
Extracted molecule total RNA
Extraction protocol Following fluorescence associated cell sorting based on CD41 and ploidy, low ploidy (8N only) and high ploidy (≥16N) megakaryocytes were pooled (52k±32k per sample) for RNA isolation using RNeasy Mini kit (Qiagen). RNA from washed platelets was isolated using TriReagent (Sigma-Aldrich).
Megakaryocyte RNA-seq libraries were prepared using SMARTer Stranded Total RNA Low Input Sample Prep kit (Clontech) and RNA-sequencing by Illumina HiSeq1500. Platelet RNA-seq libraries were prepared from 10ng of total RNA using an Ion AmpliSeq Transcriptome Mouse Gene Expression Kit and libraries were sequenced on an Ion Proton Sequencer (Thermo Fisher)
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Ion Torrent Proton
 
Description Platelets_DEG
Data processing For megakaryocyte data, the raw read were trimmed using Trimmomatic with default parameters. The reads were aligned with STAR to Ensembl mm10 reference genome. The aligned files were deduplicated using the Picard MarkDuplicates function, ["Picard Toolkit." 2019 Broad Institute, Github Repository. http://broadinstitute.github.io/picard/; Broad Institute]. To obtain levels of gene expression, read counts were generated with the Subread function FeatureCounts. Genes with 1 count per million (CPM) in at least two samples were kept for further analysis. Normalisation and differential gene expression was conducted with EdgeR.
For platelet data, Torrent Suite Software v5.6 (Thermo Fisher) was used for read processing, base calling, alignment to the reference transcriptome (mm10) and gene expression counts. Differential gene expression analysis was performed using DESeq2.
Genome_build: mm10
Supplementary_files_format_and_content: .csv file containing log-fold change, p-value, FDR and read counts for DEGs
 
Submission date Aug 03, 2020
Last update date Dec 21, 2021
Contact name Minna-Liisa Anko
E-mail(s) minni.anko@monash.edu
Organization name Monash University
Department Department of Anatomy and Developmental Biology
Street address 15 Innovation Walk
City Clayton
State/province VIC
ZIP/Postal code 3800
Country Australia
 
Platform ID GPL18635
Series (1)
GSE155620 RNA Binding Protein SRSF3 confers an essential role in megakaryocyte maturation and platelet production
Relations
BioSample SAMN15711802
SRA SRX8873894

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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