|
| Status |
Public on Jun 09, 2020 |
| Title |
myeloid progenitor cells, ASXL-MT-2 |
| Sample type |
SRA |
| |
|
| Source name |
myeloid progenitor cells
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: cord blood
cell type: myeloid progenitor cells
transduced genes: ASXL1-MT
|
| Growth protocol |
Cells were cultured in stemspan containing 10ng/ml human SCF, TPO, FLT3 ligand, GM-CSF, IL-3 and IL-6
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was prepared using RNeasy micro kit (QIAGEN).
RNA libraries were prepared using 500 ng total RNA with SureSelect Strand-Specific RNA Preparation Kit (Agilent) according to the manufacturer’s protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
ASXL1-MT rep2
|
| Data processing |
These libraries were sequenced on the Illumina HiSeq2500 System with 2×125 nucleotide paired-end reads according to the manufacturer’s protocol.
Derived reads were processed using cutadapt(1.8.1) to remove Illumina adaptor sequence.
Quality of reads was assessed using FastQC.
Processed reads were aligned to human hg19 reference transcripts using TopHat(2.1.1).
Aligned reads were counted at the gene level with featureCounts of subread-1.6.1 package to obtain gene expression profiles.
Genome_build: hg19
Supplementary_files_format_and_content: text files include FPKM values for each Sample
|
| |
|
| Submission date |
Mar 27, 2020 |
| Last update date |
Jun 09, 2020 |
| 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 |
GPL16791 |
| Series (2) |
| GSE147654 |
The effects of expression of mutant ASXL1 and HHEX on hematopoietic cells |
| GSE147656 |
Role of HHEX in hematopoietic cells |
|
| Relations |
| BioSample |
SAMN14470298 |
| SRA |
SRX8013093 |
