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| Status |
Public on Feb 13, 2024 |
| Title |
Control HSC rep2 [RNA-seq] |
| Sample type |
SRA |
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| Source name |
Hematopoietic stem cell
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6J
cell type: Hematopoietic stem cells
treatment: Sham operation
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| 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.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1500 |
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| 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.
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| Submission date |
Oct 25, 2020 |
| Last update date |
Feb 13, 2024 |
| Contact name |
Ichiro Manabe |
| E-mail(s) |
manabe-tky@umin.ac.jp
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| Organization name |
Chiba University
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| Street address |
1-8-1 Inohana, Chuo
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| City |
Chiba |
| ZIP/Postal code |
260-8670 |
| Country |
Japan |
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| Platform ID |
GPL18480 |
| Series (2) |
| GSE160066 |
Transcriptomic analyses of hematopoietic stem cells |
| GSE160068 |
Transcriptomic and epigenetic analyses of hematopoietic stem cells |
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| Relations |
| BioSample |
SAMN16547567 |
| SRA |
SRX9358339 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4859441_Control_HSC_2.ucsc.bedGraph.gz |
62.0 Mb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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