|
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 |