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Sample GSM2134551 Query DataSets for GSM2134551
Status Public on May 19, 2016
Title KO3a_FLT3_3 RNA-seq
Sample type SRA
Source name Thymus
Organism Mus musculus
Characteristics 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 For the FLT3-ITD retroviral model, 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. For the Flt3-ITD knock-in model, bulk bone marrow cells were collected.
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 2500
Description Biological replicate 3 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 (archive-2013-03-06-15-01-24) as recommended by the software developers. The gtf file was revised with novel, mouse hematopoietic lincRNA transcripts published in (doi: 10.1016/j.stem.2015.02.002).
Transcript quantification of Refseq genes and mouse hematopoetic lincRNAs was assessed by Cufflinks / Cuffdiff 2.2.1 using parameters: -b -M -p 12 -u
Genome_build: mm9
Supplementary_files_format_and_content: cufflinks.gene.counts.txt and cufflinks.transcript.counts.txt are tab separated matrices of raw gene and transcript counts, respectively. Columns names match the given Sample names in this SubSeries. The genes_plus_linc.gtf file was used for gene and transcript quantification.
Submission date Apr 27, 2016
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 GPL17021
Series (2)
GSE61969 Gene expression alterations in Dnmt3aKO/FLT3-ITD leukemia
GSE61971 Molecular profiling of mouse Dnmt3a/FLT3-ITD leukemia models
BioSample SAMN04909485
SRA SRX1733576

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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