|
| Status |
Public on Aug 31, 2021 |
| Title |
Daxx +/+ LTHSC 2 |
| Sample type |
SRA |
| |
|
| Source name |
Long-term hematopoietic stem cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: Bone marrow
mouse line: RosaCreER
genotype: Daxx +/+ Cre +/-
time after end of induction: 3 dpi
|
| 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_LTHSC_3dpi_Rosa_NormalizedCounts_Genes.txt
210215_LTHSC_3dpi_Rosa_NormalizedCounts_TE.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 |
| 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 |
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 |
|
| Relations |
| BioSample |
SAMN18167666 |
| SRA |
SRX10246419 |
