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Sample GSM1517793 Query DataSets for GSM1517793
Status Public on May 19, 2016
Title KO3a_FLT3_2 RNA-seq
Sample type SRA
Source name Bone Marrow
Organism Mus musculus
Characteristics tissue: Bone marrow
cell type: Leukemic cells
cell surface marker: CD4+;CD8+
genotype: Mx1-cre+;Dnmt3af/f;MSCV_FLT3-ITD-GFP
strain: C57BL/6
Treatment protocol PolyA selection
Growth protocol Sca1+ enriched Dnmt3a KO or WT murine bone marrow cells were transduced with retroviruses expressing MSCV-FLT3-ITD-IRES-GFP or MSCV-GFP transgenes and transplanted into lethally irradiated recipients by retro-orbital injections. Freshly sorted donor-derived mouse thymus and bone marrow cells (CD4+CD8+) from each genotype were collected from transplant recipients.
Extracted molecule total RNA
Extraction protocol Extract RNA using Qiagen Allprep DNA/RNA mini kit.
Tru-Seq RNA sample prep kit
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
Description Biological replicate 2 of Dnmt3aKO/FLT3-ITD leukemia. Donor bone marrow cells were enriched for Sca-1 prior to retroviral transduction and transplantation
Data processing Reads were aligned with Tophat 2.0.10 to both refseq transcriptome and mm9 genome using parameters: -p 12 --library-type fr-unstranded --read-realign-edit-dist 0 --min-anchor-length 6 --microexon-search --transcriptome-index=mm9_refseq. The refseq transcriptome gtf file was obtained from the Illumina iGenomes collection as recommended by the software developers
Refseq reference-based transcript assembly and transcript quantification were performed by Cufflinks 2.1.1 using parameters: --max-bundle-frags 500000 -p 16 -u -A 0.16 -b -M -g
Differential expression of Refseq genes was assessed by Cuffdiff 2.1.1 using parameters: -b -M -p 12 --min-reps-for-js-test 2 -u
Genome_build: mm9
Supplementary_files_format_and_content: gene_exp.diff is a tab separated text file of the Cuffdiff output for differential gene expression analysis of the following groups: WT double positive T cells (WT_GFP biological replicates 1, 2), FLT3-ITD leukemia (WT_FLT3 biological replicates 1, 2), and Dnmt3a knockout FLT3-ITD eluekmia (KO3a_FLT3 biological replicates 1 and 2). The remaining files are tab separated text files of the Cufflinks output for gene level expression abundance measurements produced by Cufflinks for each sample.
Submission date Oct 01, 2014
Last update date May 15, 2019
Contact name Margaret Goodell
Organization name Baylor College of Medicine
Street address One Baylor Plaza, N1030
City Houston
State/province TX
ZIP/Postal code 77030
Country USA
Platform ID GPL13112
Series (2)
GSE61969 Gene expression alterations in Dnmt3aKO/FLT3-ITD leukemia
GSE61971 Molecular profiling of mouse Dnmt3a/FLT3-ITD leukemia models
BioSample SAMN03085873
SRA SRX718848

Supplementary file Size Download File type/resource
GSM1517793_LY_2.genes.fpkm_tracking.txt.gz 704.2 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record
Processed data provided as supplementary file

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