|
| Status |
Public on Jun 30, 2016 |
| Title |
WT532 |
| 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 |
| E-mail(s) |
zhucaiying@ihcams.ac.cn
|
| 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 |
|
| Relations |
| SRA |
SRX1471734 |
| BioSample |
SAMN04326721 |
