|
| Status |
Public on Jun 21, 2022 |
| Title |
EVI1_WT_colony |
| Sample type |
SRA |
| |
|
| Source name |
Lineage- bone marrow cells in femora, tibiae and pelvis
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
cell type: bone marrow
transduced vector: pMYs-IG_3xHA-EVI1-WT
expression type: stably expressed
expression level: retroviral overexpression
|
| Treatment protocol |
none
|
| Growth protocol |
Lineage negative bone marrow cells isolated with MACS (Miltenyi) were precultured overnight and infected with pMYs-IG-EVI1-WT or +18 the next day. Three days after infection, 10,000 of GFP-sorted cells were cultured in Methocult M3434 (STEM CELL Technologies, #03434) for about 3 weeks.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using RNeasy mini kit (Qiagen) following the manufacturer’s protocol
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
RNA-seq rawdata was cleaned by FastP(PE mode) and aligned to GRCm38 by Hisat2(2.2.1)
Data were filtered using Samtools and converted to BAM files
Read counted by FeatureCount from Subreads Packages(R)
Counts data was normalized by edgeR with significant differience genes were screened out
Assembly: GRCm38
Supplementary files format and content: raw counts, Differentially expressed gene Excel
|
| |
|
| Submission date |
May 04, 2022 |
| Last update date |
Jun 21, 2022 |
| Contact name |
Masaki Nomura |
| E-mail(s) |
masaki.nomura.fbri@gmail.com
|
| Organization name |
Foundation for Biomedical Research and Innovation at Kobe
|
| Street address |
6-3-7 Minatojima Minamimachi, Chuo Ward
|
| City |
Kobe |
| State/province |
Hyogo |
| ZIP/Postal code |
650-0047 |
| Country |
Japan |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE202208 |
Aberrant EVI1 splicing contributes to EVI1-rearranged leukemia (RNA-Seq) |
| GSE202211 |
Aberrant EVI1 splicing contributes to EVI1-rearranged leukemia II |
|
| Relations |
| BioSample |
SAMN28089704 |
| SRA |
SRX15152362 |
