|
| Status |
Public on Apr 03, 2017 |
| Title |
PDX cells +DMSO after co-culture replicate 1 |
| Sample type |
SRA |
| |
|
| Source name |
patient derived AML cell line
|
| Organism |
Homo sapiens |
| Characteristics |
treatment: DMSO
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was isolated from murine EL08 and human PDX cells using the RNeasy Mini Kit (Qiagen).
cDNA was synthesized, barcoded, pooled and pre-amplified according to the UMI-seq protocol in Parekh et al. 2016. 800 pg of the cDNA pool was used for library preparation using the Nextera XT Kit (Illumina)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1500 |
| |
|
| Data processing |
Reads were tagged with UMI and sample barcode using the Drop-seq pipeline (Macosko et al., 2015).
Reads were aligned to the mouse genome mm10 and human genome hg19 using STAR 2.4.0 (Dobin et al., 2013).
Unique gene-wise counts were generated using the Drop-seq pipeline.
For data deposition, samples were demultiplexed using bamtools filter command.
Genome_build: hg19;mm10
Supplementary_files_format_and_content: sample- and gene-wise expression tables
|
| |
|
| Submission date |
Aug 24, 2016 |
| Last update date |
Jul 04, 2024 |
| Contact name |
Christoph Ziegenhain |
| E-mail(s) |
ziegenhain@bio.lmu.de
|
| Organization name |
Ludwig-Maximilians University Munich
|
| Department |
Department Biology II
|
| Lab |
Anthropology & Human genomics
|
| Street address |
Großhaderner Str. 2
|
| City |
Martinsried |
| State/province |
Bavaria |
| ZIP/Postal code |
82152 |
| Country |
Germany |
| |
|
| Platform ID |
GPL18460 |
| Series (1) |
| GSE86021 |
Crenolanib in combination with azacitidine abrogates stromal protection and survival of leukemia-initiating cells in FLT3-ITD+ AML |
|
| Relations |
| BioSample |
SAMN05617319 |
| SRA |
SRX2044206 |
