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Status |
Public on Apr 03, 2017 |
Title |
EL08 cells +AZA after co-culture replicate 2 |
Sample type |
SRA |
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Source name |
stromal cell line
|
Organism |
Mus musculus |
Characteristics |
treatment: AZA
|
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)
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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
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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 |
GPL18480 |
Series (1) |
GSE86021 |
Crenolanib in combination with azacitidine abrogates stromal protection and survival of leukemia-initiating cells in FLT3-ITD+ AML |
|
Relations |
BioSample |
SAMN05617310 |
SRA |
SRX2044227 |