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| Status |
Public on Jun 20, 2018 |
| Title |
Nifedipine-4 |
| Sample type |
SRA |
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| Source name |
hematopoietic stem cells
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: Bone marrow
age: 8-10 weeks
genotype: wild type
cell type: HSC
treatment: Nifedipine
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| Extracted molecule |
total RNA |
| Extraction protocol |
After 100 cells were sorted, first strand cDNA were synthesized followed by generating 2nd strand by minorly modified method that was previousely reported (Hiyashi et al. Nature Communication, 2018: 9) .
Using Nextera XT DNA sample Prep Kit (Illumina Inc., San Diego, CA), libraries were prepared by minorly modified method that was previousely reported (Hiyashi et al. Nature Communication, 2018: 9) .
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
mRNA profile generated by deep sequencing using Illumina Next-Seq 500
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using CLC genomic workbench v.11.0.0
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated by CLC genomic workbench v.11.0.0
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include read number and RPKM values for each Sample.
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| Submission date |
Feb 26, 2018 |
| Last update date |
Jun 20, 2018 |
| Contact name |
Terumasa Umemoto |
| Organization name |
Kumamoto University
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| Street address |
2-2-1, Honjo, Chuo-Ku
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| City |
Kumamoto |
| ZIP/Postal code |
862-0957 |
| Country |
Japan |
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| Platform ID |
GPL19057 |
| Series (1) |
| GSE111118 |
mRNA profiles of active hematopoieitc stem cells |
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| Relations |
| BioSample |
SAMN08606651 |
| SRA |
SRX3742152 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3022360_A7_S7_L001_R1_001.txt.gz |
767.4 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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