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Sample GSM5723354 Query DataSets for GSM5723354
Status Public on Dec 08, 2021
Title young MPP4 3h
Sample type SRA
 
Source name 10 week multipotent progenitor 4s after cytokine stimulation (3h)
Organism Mus musculus
Characteristics cell type: Murine bone marrow derived MPP4s
surface markers: IL-7- Lin- Sca-1+ c-kit+ CD34+ CD150- CD48+ Flt3+
age: 10-week-old
strain: C57BL/6
treatment: cytokine stimulation(3h)
Treatment protocol Young and aged cells 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
 
Description young MPP4 after cytokine stimulation(3h)
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
Supplementary_files_format_and_content: TPM_gene.txt, gene_norm_count_ntd.txt
 
Submission date Dec 08, 2021
Last update date Dec 09, 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
GSE190422 Epigenetic traits inscribed in chromatin accessibility in aged hematopoietic stem cells (RNA-seq of MPPs after cytokine stimulation)
Relations
BioSample SAMN23771532
SRA SRX13351113

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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