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Sample GSM5536893 Query DataSets for GSM5536893
Status Public on Aug 28, 2021
Title AATGTA_DUX4
Sample type SRA
 
Source name ALL PDX line
Organism Homo sapiens
Characteristics cell type: patient derived xenograft (PDX) cells
disease state: acute lymphoblastic leukemia
protocol: PDX cells injected into NSG mice
treatment: mice treated with shDUX4_TAM
sample type: DUX4 KD PDX cells isolated from murine bone marrow after treatment
Treatment protocol Mice were treated with 100 mg/kg tamoxifen 7 and 8 days after injection to induce recombination and shRNA expression
Growth protocol PDX cells were injected into NSG mice
Extracted molecule total RNA
Extraction protocol prime-seq
Library was constructed using the prime-seq protocol
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 1500
 
Data processing Fastq reads were processed with the zUMIs pipeline (Parekh et al., 2017)
cDNA reads were aligned toa combined Human Genome (hg38) and Mouse Genome (mm10) with STAR 2.6.0a
Quantification was done with ENSEMBL gene models (Homo_sapiens:GRCh38.84, Mus_musculus:GRCm38.85)
Mouse reads were excluded for further analysis
Genome_build: hg38
Supplementary_files_format_and_content: UMI_counts.txt: cell (columns) and gene (rows) -wise UMI expression table
 
Submission date Aug 25, 2021
Last update date Aug 28, 2021
Contact name Irmela Jeremias
E-mail(s) irmela.jeremias@helmholtz-muenchen.de
Organization name Helmholtz Zentrum Mùˆnchen, German Center for Environmental Health (HMGU), Munich, Germany
Department Research Unit Apoptosis in Hematopoietic Stem Cells
Street address Feodor-Lynenstr. 21
City Munich
ZIP/Postal code 81377
Country Germany
 
Platform ID GPL18460
Series (1)
GSE182780 RNA sequencing of patient derived xenograft sample ALL-811 using prime-seq
Relations
BioSample SAMN20972845

Supplementary data files not provided
Raw data not provided for this record
Processed data are available on Series record

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