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Sample GSM5137349 Query DataSets for GSM5137349
Status Public on Aug 31, 2021
Title Daxx F/F MPP4 1
Sample type SRA
Source name Lymphoid-committed multipotent progenitor
Organism Mus musculus
Characteristics strain: C57BL/6
tissue: Bone marrow
mouse line: Mx1Cre
genotype: Daxx F/F Cre +/-
time after end of induction: 3 wpi
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 NovaSeq 6000
Description 210215_MPP_3wpi_NormalizedCounts_Gene.txt
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 Mar 05, 2021
Last update date Aug 31, 2021
Contact name Paolo Salomoni
Organization name DZNE e.V.
Street address Sigmund-Freud-Str. 27
City Bonn
ZIP/Postal code 53127
Country Germany
Platform ID GPL24247
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
BioSample SAMN18167746
SRA SRX10246452

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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