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Sample GSM2691084 Query DataSets for GSM2691084
Status Public on Dec 07, 2020
Title BaF3+BCR-Abl treated with DMSO replicate 1
Sample type SRA
Source name Cell line
Organism Mus musculus
Characteristics strain: C3H 
cell line: BaF3 pro B cells
genotype/variation: expressing BCR-Abl
agent: control
Treatment protocol BaF3 cells expressing BCR-Abl were treated with 20µM DJ-34 (investigational drug) or DMSO control for 6 hrs.
Growth protocol BaF3 cells expressing BCR-Abl were cultured on RPMI-1640 medium supplemented with 10% heat inactivated FBS and 1% Pen/strep.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted by RNeasy mini kit Qiagen followed by DNase I treatment in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyzer.
RNA libraries were prepared for sequencing using standard Illumina protocols
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 4000
Data processing Clean reads (as provided by BGI) were mapped to the GRCm38.85 genome assembly using Tophat2 (v. 2.1.1), then using default options BAM files were indexed using SAMtools.
Differential expression data was produced using cuffquant and cuffdiff with default options, from the cufflinks suite (v 2.2.1 / SVN rev 4237).
Reference genome for the primary assembly and gene annotations used are revision 85 of GRCm38, from
Genome_build: GRCm38.85 genome assembly
Supplementary_files_format_and_content: xlsx format with raw gene count, average gene count and FPKM values for each sample.
.tdf files were used for visualization in IGV.
Submission date Jun 30, 2017
Last update date Dec 07, 2020
Contact name Jorrit Enserink
Organization name The Norwegian Radium Hospital
Department Molecular Cell Biology
Street address Ullernchausseen 70
City Oslo
ZIP/Postal code N-0379 Oslo
Country Norway
Platform ID GPL21103
Series (1)
GSE100678 A cell competition-based drug screen identifies a novel compound that targets c-Myc addiction of leukemia cells
BioSample SAMN07303435
SRA SRX2973185

Supplementary file Size Download File type/resource
GSM2691084_control-2_accepted_hits.bam.tdf 34.1 Mb (ftp)(http) TDF
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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