|
Status |
Public on Apr 10, 2015 |
Title |
LFS1-A_day0 |
Sample type |
SRA |
|
|
Source name |
LFS-derived MSCs
|
Organism |
Homo sapiens |
Characteristics |
disease/genotype: Li-Fraumeni Syndrome (LFS) patient source cell type: patient-derived iPSCs cell subtype: mesenchymal stem cells (MSCs) time point: day 0 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 |
SAMN02808384 |
SRA |
SRX556311 |