 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Dec 20, 2019 |
| Title |
HSCs, [Ca2+]high-4 |
| Sample type |
SRA |
| |
|
| Source name |
Hematopoietic stem cell
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: bone marrow
cell type: Hematopoietic stem cell (HSC)
cell population: [Ca2+]high
|
| Extracted molecule |
total RNA |
| Extraction protocol |
One hundred [Ca2+]high HSCs and [Ca2+]low HSCs were sorted into RNA lysis buffer. The first strand of cDNA was synthesized by using PrimeScript RT reagent kit (TaKaRa Bio Inc.) and not-so random primers. Following the synthesis of the first strand, the second strand was synthesized by using Klenow Fragment (3’, -5’, exo-; New England Biolabs Inc.) and complement chains of not-so random primers. Using purified double-strand cDNA, the library for RNA-Seq was prepared and amplified using Nextera XT DNA sample Prep kit (Illumina Inc.).
These prepared libraries were sequenced on Next-Seq system (Illumina Inc.), according to the manufacturer’s instruction.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Each obtained read was mapped to the reference sequence “GRCm38/mm10” using CLC genomic workbench v11.0.0 (Qiagen), and expression levels were normalized and subjected to the statistical analyses based on EdgeR.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample
|
| |
|
| Submission date |
Oct 15, 2019 |
| Last update date |
Dec 20, 2019 |
| Contact name |
Tsuyoshi Fukushima |
| E-mail(s) |
[email protected]
|
| Organization name |
Institute of Medical Science
|
| Department |
Cell therapy
|
| Street address |
siroganedai 4-6-1
|
| City |
minato-ku |
| State/province |
tokyo |
| ZIP/Postal code |
108-8639 |
| Country |
Japan |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE138884 |
Discrimination of dormant and active hematopoietic stem cells by G0 markers reveals dormancy regulation by cytoplasmic calcium |
|
| Relations |
| BioSample |
SAMN13032253 |
| SRA |
SRX6994029 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4121234_Calcium-high-4.txt.gz |
228.1 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
