|
| Status |
Public on Jun 28, 2012 |
| Title |
TGCGGA |
| Sample type |
SRA |
| |
|
| Source name |
FB
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Fibroblasts
treatment: Chondrogenesis
day: d7
patient code name: Charlotte
barcode: TGCGGA
|
| Treatment protocol |
Passage three or four cells were plated 72 hours prior to induction of differentiation. 10% FBS and 1% penicillin-streptomycin containing growth medium was supplemented with: 1µM dexamethasone, 500µM IBMX (3-isobutyl-1methylxanthine), 100µM indomethacin and 10µg/ml insulin for adipogenic induction; 100nM dexamethasone, 50µM L-ascorbic acid 2-phosphate and 10mM glycerol 2-phosphate for osteogenic induction; 50µM L-ascorbic acid 2-phosphate, 6,25µg/ml insulin and 10ng/ml TGFbeta-1 (Peprotech) for chondrogenic induction.
|
| Growth protocol |
MSCs were isolated from human subcutaneous adipose tissue, passed through a 100 µm nylon mesh and replated in 10% FBS growth medium. After 48 h medium was replaced to remove non-adherent cells. Further cultivation was performed under standard cell culture conditions. Fibroblasts were isolated from dermal skin of the same donors as MSCs and primary culture was established by fibroblast outgrowth from skin explants placed onto Primaria dish (BD Falcon) in 10% FBS and 1% penicillin-streptomycin DMEM-High Glucose (Gibco) growth medium.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Trizol (Invitrogen). Following a phenol/chloroform extraction and isopropanol precipitation, RNA samples were treated with DNase I using DNA-free kit (Ambion). RNA-seq libraries were prepared according to the STRT protocol ("Highly multiplexed and strand-specific single-cell RNA 5′ end sequencing" Islam et al. Nature Protocols vol. 7 no. 5, 2012)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
CAGE |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
C11
|
| Data processing |
Base-calling was performed using CASAVA on the Genome Analyzer IIx
Raw reads were demultiplexed into 96 files (one per barcode, but 4 barcodes were unused)
Reads were aligned using Bowtie version 0.12.7 with standard parameters
Reads were then annotated using gene models obtained from UCSC on 2012-02-03.
Genome_build: hg19
Supplementary_files_format_and_content: RPM (reads per million) was calculated by considering all reads mapped onto all known exons of each gene (including spliced reads)
Supplementary_files_format_and_content: L127_RPM.tab (supplementary) contains a matrix of RPM values for each sample and each gene, in tab-delimited text format
|
| |
|
| Submission date |
Apr 23, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Sten Linnarsson |
| E-mail(s) |
sten.linnarsson@ki.se
|
| Phone |
+46852487577
|
| URL |
http://ki.se
|
| Organization name |
Karolinska Institutet
|
| Department |
MBB
|
| Lab |
Molecular Neurobiology
|
| Street address |
Scheeles väg 2
|
| City |
Stockholm |
| ZIP/Postal code |
17177 |
| Country |
Sweden |
| |
|
| Platform ID |
GPL10999 |
| Series (1) |
| GSE37521 |
RNA-Seq Analysis Reveals Different Dynamics of Differentiation of Human Dermis- and Adipose-derived Stromal Stem Cells |
|
| Relations |
| SRA |
SRX144148 |
| BioSample |
SAMN00862525 |
