|
| Status |
Public on Jul 23, 2024 |
| Title |
PBS_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
CMM
|
| Organism |
Mus musculus |
| Characteristics |
cell line: CMM
cell type: AML
treatment: PBS
|
| Treatment protocol |
start treatment when %GFP+ leukemia cells reached ~1% in blood, treat mice IV with PBS/CpG-scrODN/CpG-STAT3dODN every other day for 3 times
|
| Growth protocol |
CMM (GFP+) cells IV engrafted in C57BL/6 mice
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Harvest spleen 1 day post last treatment and make single cell suspension, enrich c-Kit+ leukemia cells using STEMCELL EasySep™ PE Positive Selection Kit, extract RNA using Promega Maxwell RSC simplyRNA kit.
RNA libraries for RNA-seq were prepared illumina RNA-seq Library Prep Kit following manufacturer's protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
RNAseq reads were aligned to the mouse reference genome (mm10) using the TopHat (v.1.3.1).
RNAseq expression was quantified as reads per kilo base of total exon length per million mapped (RPKM) reads using Partek Genomics Suite v.6.12.0713. Minimally expressed genes (<0.1 RPKM) were excluded. Gene Expression measurement was log2 transformed with 0.01 offset for differential gene expression analysis using ANOVA with FDR<0.05 and fold change >1.5.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample
|
| |
|
| Submission date |
May 21, 2023 |
| Last update date |
Jul 23, 2024 |
| Contact name |
Haiqing Li |
| E-mail(s) |
hali@coh.org
|
| Organization name |
City of Hope National Medical Center
|
| Department |
Shared Resources Department
|
| Lab |
Integrative Genomics Core Lab
|
| Street address |
1500 E Durate Rd
|
| City |
Duarte |
| State/province |
CA |
| ZIP/Postal code |
91010 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE233096 |
STAT3 inhibition permits epigenetic reprogramming and TLR9/IRF8-driven differentiation of inv(16) acute myeloid leukemia [RNASEQ_AML_DECSCR] |
| GSE233099 |
STAT3 inhibition permits epigenetic reprogramming and TLR9/IRF8-driven differentiation of inv(16) acute myeloid leukemia. |
|
| Relations |
| BioSample |
SAMN35301423 |
| SRA |
SRX20461995 |
