|
| Status |
Public on May 25, 2018 |
| Title |
ASXL1-MT rep3 |
| Sample type |
SRA |
| |
|
| Source name |
Bone marrow progenitor cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: Bone marrow progenitor cells
age: 8- to 12-week-old
transduced genes: ASXL1-MT
|
| Growth protocol |
Cells were cultured in M3234 methylcellulose containing 20 ng/ml SCF, 10 ng/ml IL-3 and 10 ng/ml IL-6 according to manufacturer’s instructions.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was prepared using RNeasy mini kit (QIAGEN).
RNA libraries were prepared for sequencing using NEBNext Ultra Directional RNA Library Prep Kit for Illumina according to the manufacturer's protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were mapped to the mouse genome (mm10) using TopHat v2.0.9, with default parameters.
Normalized read counts were calculated using HTSeq 0.6.1p1 (-s reverse -m intersection-strict) and DESeq22 1.6.3 with VST normalization.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each Sample.
|
| |
|
| Submission date |
May 24, 2018 |
| Last update date |
May 25, 2018 |
| Contact name |
Shuhei Asada |
| Organization name |
Institute of Medical Science, The University of Tokyo
|
| Department |
Cellular Therapy
|
| Lab |
Kitamura Lab
|
| Street address |
4-6-1 Shirokanedai, Minato-ku
|
| City |
Tokyo |
| ZIP/Postal code |
1088639 |
| Country |
Japan |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE114861 |
The effects of mutant ASXL1 and BAP1 expression on hematopoietic cells |
|
| Relations |
| BioSample |
SAMN09246027 |
| SRA |
SRX4119898 |
