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Sample GSM4859440 Query DataSets for GSM4859440
Status Public on Feb 13, 2024
Title Control HSC rep1 [RNA-seq]
Sample type SRA
Source name Hematopoietic stem cell
Organism Mus musculus
Characteristics strain: C57BL/6J
cell type: Hematopoietic stem cells
treatment: Sham operation
Extracted molecule total RNA
Extraction protocol Bone marrow cells were harvested from tibias, femurs, pelvis, and vertebrae by crushing with a mortar and pestle in MACS buffer (PBS supplemented with 0.5% bovine serum albumin and 2 mM EDTA). The cells were passed through a 25G needle several times and filtered with a 70 μm cell strainer. After washed and filtered with a 40 μm cell strainer, the samples were incubated with Mouse CD117 Microbeads (Miltenyi) and separated by autoMACS (Miltenyi). Isolated cells in positive selection were mixed with antibodies for flow cytometry. CD45+ Lin- Sca1+cKit+CD34-Flt3-CD150+CD48- cells were sorted as HSCs. Sorted cells were lysed in Buffer RLT plus (QIAGEN) and RNA was harvested using RNeasy micro Kit (QIAGEN).
Poly-A mRNA was extracted from total RNA by using an Oligo-dT beads of NEBNext Poly(A) RNA Magnetic Isolation Module (NEB), after which RNA-seq libraries were prepared using a NEBNext Ultra II RNA Library Preo Kit for Illumina (NEB) according to the manufacturer’s protocol.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 1500
Data processing Reads were aligned to the mm10 mouse genome using STAR.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: bedGraph files were generated using Homer.
Submission date Oct 25, 2020
Last update date Feb 13, 2024
Contact name Ichiro Manabe
Organization name Chiba University
Street address 1-8-1 Inohana, Chuo
City Chiba
ZIP/Postal code 260-8670
Country Japan
Platform ID GPL18480
Series (2)
GSE160066 Transcriptomic analyses of hematopoietic stem cells
GSE160068 Transcriptomic and epigenetic analyses of hematopoietic stem cells
BioSample SAMN16547555
SRA SRX9358338

Supplementary file Size Download File type/resource
GSM4859440_Control_HSC_1.ucsc.bedGraph.gz 73.9 Mb (ftp)(http) BEDGRAPH
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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