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Sample GSM2912567 Query DataSets for GSM2912567
Status Public on Dec 29, 2020
Title Healthy hemeostatic MSC3
Sample type SRA
 
Source name MSC
Organism Mus musculus
Characteristics strain: C57BL/6
tissue: Bone marrow
Treatment protocol Target cells were sorted from the nucleated cell mixtures of bone marrow and compact bones.
Growth protocol All mice in this study were kept in C57BL/6J backgroud. MSCs were sorted from pre-leukemic mice, control mice, and MSC-treated pre-leukemic mice.
Extracted molecule polyA RNA
Extraction protocol The procedure of RNA extraction and reverse transcription into double-stranded DNA is based on published methods(PMID:20203668).
Libraries were prepared according to Illumina's instructions accompanying the illumina Nextera XT DNA Sample Preparation Kit (FC-131-1096).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Data processing Bcl2fastq convert .bcl files into fastq files
Fastq files were aligned to mm10 genome.*.bt2 files to generate accepted_hits.bam file by tophat, and the used cuffquant scripts (cufflinks-2.2.1) to calculated genes expression level.
Gene expression levels of different samples were normalized by cuffnorm scripts (cufflinks-2.2.1), and finally generated genes.fpkm_table
Genome_build: mm10
Supplementary_files_format_and_content: fpkm_table was generated by cuffnorm
Supplementary_files_format_and_content: gene expression value
 
Submission date Jan 03, 2018
Last update date Dec 29, 2020
Contact name Xia Chengxiang
E-mail(s) xia_chengxiang@gibh.ac.cn
Phone 15626209179
Organization name GIBH
Street address Kai Yuang Road 190
City Guangzhou
State/province Guangdong
ZIP/Postal code 510530
Country China
 
Platform ID GPL19057
Series (2)
GSE108725 Mesenchymal stromal cells orchestrate the overhaul of leukemia bone marrow microenvironment via educating macrophages
GSE125029 Mesenchymal stromal cells orchestrate the overhaul of leukemia bone marrow microenvironment via educating macrophages
Relations
BioSample SAMN08289089
SRA SRX3582970

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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