|
| Status |
Public on Aug 20, 2018 |
| Title |
D5(39Y)-3 |
| Sample type |
SRA |
| |
|
| Source name |
fibroblast induced D5
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: fibroblast induced D5
|
| Treatment protocol |
Fibroblasts were treated by small molecule cocktail for 12 days,and treated for 5 days were denoted as fibroblast induced D5, for 12 days denoted as fibroblast induced D12, and on day 15 denoted as mesenchymal stem cell-LC D15.
|
| Growth protocol |
Human fibroblast cells and fibroblast-derived cells till 15 days were routinely maintained in DMEM (Hyclone) with 10% fetal bovine serum(BI), bone mesenchymal stem cell and MSC-LC were cultured in MSC medium(MSC medium (Cyagen, HUXMA-90011) for expansion.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
A total amount of 2 μg RNA per sample was used as input material for the RNA sample preparations.mRNA was purified from total RNA using poly-T oligo-attached magnetic beads.
Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (#E7530L, NEB, USA) according to the instruction manual.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Description |
W04
|
| Data processing |
Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was mapped to the reference genome (hg19) using TopHat v2.0.12.
Reads Count for each gene in each sample was counted by HTSeq v0.6.0.Fragment per kilobases per million mapped reads were calculated by Cufflinks(v2.2.1).
Genome_build: hg19
Supplementary_files_format_and_content: "counts.csv" containes gene counts;"fpkm.csv" contains gene fpkm values.
|
| |
|
| Submission date |
Aug 23, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Kunshan Zhang |
| E-mail(s) |
[email protected]
|
| Organization name |
Tongji Hospital, Tongji University
|
| Department |
Stem cell Translational Research center
|
| Street address |
389 Xincun Road
|
| City |
Shanghai |
| ZIP/Postal code |
200092 |
| Country |
China |
| |
|
| Platform ID |
GPL20795 |
| Series (1) |
| GSE102983 |
Rejuvenation and conversion of skin fibroblasts for immune modulation and bone and cartilage repair in vivo |
|
| Relations |
| BioSample |
SAMN07545979 |
| SRA |
SRX3118442 |
