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Sample GSM1888856 Query DataSets for GSM1888856
Status Public on Sep 21, 2015
Title Mxplus_Smc3het_Flt3ITD_RNA_2
Sample type SRA
 
Source name c-Kit+ cells purified from bone marrow
Organism Mus musculus
Characteristics tissue: bone marrow
cell type: c-Kit+ cells
genotype: Smc3 fl/del Flt3-ITD
Growth protocol Whole bone marrow from individual mice was positively selected for Cd117 (c-Kit) using antibody-conjugated magnetic beads (Cd117 microbeads, Miltenyi Biotec Inc).
Extracted molecule polyA RNA
Extraction protocol Total RNA was isolated using Trizol (Invitrogen), and cDNA was synthesized using the SuperScript First-Strand kit (Invitrogen). Sequencing libraries were constructed using the Nextflex Rapid Directional RNA-seq kit (Bioo Scientific).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Description Flt3Smc3het_RNA_Seq_1
Cells were purified from whole bone marrow 4-weeks following PIpC injection; mice harbor Mx1-cre, floxed Smc3, and Flt3-ITD alleles
Data processing expression levels: Gene-level expression measurements for 23,021 Ensembl mouse genes were reported in fragments per kilobase per million reads (FPKM) by Cufflinks 2.0.0 (http://cufflinks.cbcb.umd.edu/) (Trapnell et al., 2010). Cufflinks assembles transcripts, estimates their abundance, and tests for differential expression and regulation in RNA-Seq samples. Cufflinks command line-cufflinks --GTF <gtf_file> -q -p 3 -u -b <genome.fa> -o <output directory> <bam_file_from_tophat>
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM files for each sample
 
Submission date Sep 18, 2015
Last update date May 15, 2019
Contact name James Bradner
E-mail(s) bradner_computation@dfci.harvard.edu
Organization name Dana-Farber Cancer Institute
Department Medical Oncology
Lab Bradner Lab
Street address 450 Brookline
City Boston
State/province MA
ZIP/Postal code 02215
Country USA
 
Platform ID GPL13112
Series (2)
GSE73216 Dose-dependent role of the cohesin complex in normal and malignant hematopoiesis [RNA-Seq]
GSE73218 Dose-dependent role of the cohesin complex in normal and malignant hematopoiesis
Relations
BioSample SAMN04096896
SRA SRX1262257

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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