|
| Status |
Public on Apr 10, 2015 |
| Title |
LFS1-A_day7 |
| Sample type |
SRA |
| |
|
| Source name |
LFS-derived MSCs intermediate
|
| Organism |
Homo sapiens |
| Characteristics |
disease/genotype: Li-Fraumeni Syndrome (LFS) patient
source cell type: patient-derived iPSCs
cell subtype: mesenchymal stem cells (MSCs) intermediate
time point: day 7 of osteoblast differentiation treatment
|
| Treatment protocol |
mesenchymal stem cells were differentiated to osteoblasts by culturing with osteogenic differentiation media: alphaMEM supplemented with 0.1 μM dexamethason, 10mM beta-glycerol phosphate, 200 μM ascorbic acid and 10% fetal bovine serum.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were sorted by FACS and RNA was isolated using Trizol reagent.
Illumina TruSeq RNA Sample Prep Kit was used with up to 2 ug of total RNA for the construction of sequencing libraries Illumina protocols with the exception of the multiplexing barcodes introduction at the PCR amplification stage.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
fibroblast derived induced pluripotent stem cell
|
| Data processing |
Illumina Casava 1.8.2 software used for basecalling and demultiplexing.
Sequence library reads were trimmed for adapter sequence, low quality and low complexity reads removed using FASTX-toolkit suite
Alignment to hg19 using Tophat release 2.0.9 and Bowtie2 release2.1.0
Differential expression performed with Cufflinks release 2.1.1 and Homo sapiens hg19 reference annotation
Genome_build: hg19
Supplementary_files_format_and_content: MSCtoOB experiment FPKM tables derived from Cufflinks cuffdiff output MSCtoOB_FPKM.txt output tab-delimited file. See reference at http://cufflinks.cbcb.umd.edu/manual.html#fpkm_track and Trapnell et al. Nat Biotech 2010.
|
| |
|
| Submission date |
May 30, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Betty Chang |
| E-mail(s) |
filipe.pereira@uc-biotech.pt
|
| Organization name |
Mount Sinai School of Medicine
|
| Street address |
1425 Madison Ave
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10029 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE58123 |
Modeling Familial Cancer with iPSC Approaches |
|
| Relations |
| BioSample |
SAMN02808389 |
| SRA |
SRX556312 |
