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Sample GSM3369674 Query DataSets for GSM3369674
Status Public on Aug 31, 2021
Title Daxx F/F GMP 2 [3428]
Sample type SRA
 
Source name Hematopoietic Progenitor Cell
Organism Mus musculus
Characteristics strain: C57BL/6
tissue: Bone marrow
genotype: Daxx F/F Cre +/-
Extracted molecule total RNA
Extraction protocol Primary hematopoietic stem/progenitor cells were isolated form bone marrow and populations sorted by flow cytometry. Total RNA was extracted using Trizol reagent.
Illumina sequencing libraries were created with the Ovation SoLo RNA-seq kit from NuGEN Technologies according to the manufacturer's instructions.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 1500
 
Description 180829_GMP_NormalizedCounts_AllGenes.txt
180829_GMP_NormalizedCounts_TEtranscripts.txt
3428
Data processing Illumina Casava 1.8.4 for base calling and demultiplexing
Sequencing reads were adapter trimmed using Cutadapt 1.13 and aligned against mm10 (GENCODE release M14) using STAR aligner 2.5.3 with standard settings. For repeat element analysis STAR aligner was run with the following options: --outFilterMultimapNmax 100 --winAnchorMultimapNmax 100.
Reads mapping to rRNA, the mitochondrial genome and non-uniquely were removed. For repeat element expression analysis only reads mapping to the mitochondrial genome were removed.
Differentially expressed genes and repeat elements were obtained by running DESeq2 1.16.1.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited file with DESeq2 normalized counts for each sample
 
Submission date Aug 31, 2018
Last update date Aug 31, 2021
Contact name Paolo Salomoni
E-mail(s) paolo.salomoni@dzne.de
Organization name DZNE e.V.
Street address Sigmund-Freud-Str. 27
City Bonn
ZIP/Postal code 53127
Country Germany
 
Platform ID GPL18480
Series (2)
GSE119308 Aberrant chromatin landscape upon loss of the H3.3 chaperone Daxx leads to Pu.1-mediated neutrophilia and inflammation [RNA-Seq]
GSE119309 Aberrant chromatin landscape upon loss of the H3.3 chaperone Daxx leads to Pu.1-mediated neutrophilia and inflammation
Relations
BioSample SAMN09940167
SRA SRX4628169

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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