|
| Status |
Public on Mar 19, 2021 |
| Title |
aged HSC 12 hour |
| Sample type |
SRA |
| |
|
| Source name |
20 month hematopoietic stem cells
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Murine bone marrow derived HSCs
surface markers: IL-7- Lin- Sca-1+ c-kit+ CD34- CD150+ CD48- Flt3-
age: 20-month-old
strain: C57BL/6
treatment: 12 hours after cytokine stimulation
|
| Treatment protocol |
Young and aged HSCs were stimulated with a mixture of cytokines (SCF, TPO, GM-CSF, IL-1, IL-6, and IL-11) (BioLegend) in S-Clone SF-O3 (Sanko Junyaku) supplemented with 10% FBS, 50 μM 2-ME, and 1% GPS
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using RNeasy Plus Micro Kit (Qiagen)
Total RNA were subjected to reverse transcription and amplification with a SMARTer Ultra Low Input RNA Kit for Sequencing (Clontech). After sonication with an ultrasonicator (Covaris), the libraries for RNA-seq were generated from fragmented DNA with 8 cycles of amplification using a NEB Next Ultra DNA Library Prep Kit (New England BioLabs). After the libraries were quantified using the Bioanalyzer (Agilent), samples were subjected to sequencing with Hiseq1500 (Illumina) and 61 cycles of the sequencing reactions were performed.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1500 |
| |
|
| Data processing |
alignment:TopHat2 (version 2.0.13; with default parameters) and Bowtie2 (version 2.1.0) were used for alignment to the reference mouse genome (mm10 from the University of California, Santa Cruz Genome Browser;) with annotation data from iGenomes (Illumina)
Row count for each gene symbol are generated by StringTie
Data normalization:DESeq2
DESeq2 were used to perform statistical analysis for differentially expressed genes
Genome_build: mm10
|
| |
|
| Submission date |
Mar 19, 2021 |
| Last update date |
Mar 20, 2021 |
| Contact name |
Atsushi Iwama |
| Organization name |
The Institute of Medical Science, The University of Tokyo
|
| Department |
Center for Stem Cell Biology and Regenerative Medicine
|
| Lab |
Division of Stem Cell and Molecular Medicine
|
| Street address |
4-6-1, Shirokanedai
|
| City |
Minato-ku |
| State/province |
Tokyo |
| ZIP/Postal code |
108-8639 |
| Country |
Japan |
| |
|
| Platform ID |
GPL18480 |
| Series (2) |
| GSE162662 |
Epigenetic traits inscribed in chromatin accessibility in aged hematopoietic stem cells |
| GSE169206 |
Epigenetic traits inscribed in chromatin accessibility in aged hematopoietic stem cells (RNA-seq of HSCs after cytokine stimulation) |
|
| Relations |
| BioSample |
SAMN18356035 |
| SRA |
SRX10382325 |
