|
| Status |
Public on Dec 05, 2020 |
| Title |
RNA-seq aged MPP2 rep1 |
| Sample type |
SRA |
| |
|
| Source name |
20 month multipotent progenitor 2s
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Murine bone marrow derived MPP2s
surface markers: IL-7- Lin- Sca-1+ c-kit+ CD34+ CD150+ CD48+ Flt3-
age: 20-month-old
strain: C57BL/6
|
| 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 |
Dec 03, 2020 |
| Last update date |
Dec 05, 2020 |
| 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) |
| GSE162607 |
Epigenetic traits inscribed in chromatin accessibility in aged hematopoietic stem cells (RNA-seq) |
| GSE162662 |
Epigenetic traits inscribed in chromatin accessibility in aged hematopoietic stem cells |
|
| Relations |
| BioSample |
SAMN16988374 |
| SRA |
SRX9626672 |
