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Sample GSM1968343 Query DataSets for GSM1968343
Status Public on Jun 30, 2016
Title WT535
Sample type SRA
Source name WT_BM-derived MSPCs
Organism Mus musculus
Characteristics strain background: C57BL/6
genotype/variation: Wild type
cell type: BM-derived Mesenchymal stem/progenitor cells (MSPCs)
passages: 5-10
Growth protocol Bone marrow–derived mesenchymal stem/progenitor cells were cultured with MSC medium (MesenCult basal media plus 20% of MesenCult Supplemental), and replated when the cultures reached 80-90% confluency.
Extracted molecule total RNA
Extraction protocol 2x10^6 MSPCs were harvested and total RNA was extracted using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
Data processing aligement use Tophat:tophat-2.0.3.Linux_x86_64 with parameters -p 4 -G --splice-mismatches 2 --max-multihits 1 --min-intron-length 20 --library-type fr-unstranded
abundance measurements use cufflinks:cufflinks-2.2.1.Linux_x86_64 with parameters -p 4 -v -u -G
differential expression use cuffdiff:versions cufflinks-2.2.1.Linux_x86_64/cuffdiff ,with parameters -p 5 --library-type fr-unstranded -m 400
DAVID functional annotation use differential expression gene between WT and KO
Gene set enrichment anslysis(GSEA) use gene profiling generated from cofflinks.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample,differentiation experssion gene between WT and KO
Submission date Dec 08, 2015
Last update date May 15, 2019
Contact name Caiying Zhu
Phone 13622053408
Organization name Institute of Hematology & Blood Diseases Hospital
Street address NO. 288 Nanjing Road, Heping District, Tianjin
City Tianjin
ZIP/Postal code 300020
Country China
Platform ID GPL17021
Series (2)
GSE75787 Loss of Asxl1 Alters Self-Renewal and Cell Fate of Bone Marrow Stromal Cell
GSE75788 Loss of Asxl1 Alters Mesenchymal Stem Cell Fate through H3K4me3
SRA SRX1471735
BioSample SAMN04326722

Supplementary file Size Download File type/resource
GSM1968343_WT535_genes.fpkm_tracking.gz 777.7 Kb (ftp)(http) FPKM_TRACKING
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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