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Sample GSM4955273 Query DataSets for GSM4955273
Status Public on Dec 05, 2020
Title RNA-seq aged CLP rep1
Sample type SRA
 
Source name 20 month common lymphoid progenitor
Organism Mus musculus
Characteristics cell type: Murine bone marrow derived CLPs
surface markers: IL-7+ Lin- Sca-1 low c-kit low
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 SAMN16988368
SRA SRX9626682

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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