|
| Status |
Public on Mar 23, 2015 |
| Title |
MSC_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
mesenchymal stem cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: bone marrow mesenchymal stem cells (Capelli et al; BM Transpl, 2007)
|
| Growth protocol |
HK2 cells and /or CL17 cells were cultured in Keratinocyte Serum Free medium (Clonetics, Life Technologies) supplemented with Bovine Pituitary Extract (BPE) and Epidermal Growth Factor (EGF). MSC were cultured in DMEM low glucose, supplemented with 5% human platelet lysate according to (Capelli et al; BM Transpl, 2007).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was prepared from MSC, HK2 cells and five of the clones obtained by limiting dilution, using TRIzol reagent according to the manufacturer’s instructions.
PolyA+ RNA was obtained from 20µg of total RNA using Dynabeads® mRNA DIRECT™ Micro Kit after adding external RNA spike-in controls (ERCC). Libraries were prepared using the Ion Total RNA-Seq Kit v2. Template preparation and sequencing were performed using the Ion PGM™ Template OT2 200 Kit and the Ion PGM™ Sequencing 200 Kit v2. Each replicate was sequenced on the Ion PGM™ Sequencer using a Ion 318™ Chip.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Ion Torrent PGM |
| |
|
| Data processing |
Data extraction, base calling and trimming for adaptor sequences were performed using TorrentSuite™ Software 3.6
Alignment to whole genome (version hg19) was performed using TorrentSuite™ Software 3.6 with default parameters.
To count reads overlapping with known exon coordinates (RefSeq, UCSC) we used the HTSeq software through a modified version of the FeatureCounter plugin that allowed to discard reads with mapping quality score <5. Regions of two or more overlapping genes that lay on the same strand were analyzed as different transcipts. Genes/trascribed regions with mean read count <5 in the 2 replicates have been filtered out.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample.
|
| |
|
| Submission date |
Apr 08, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Paraskevas Iatropoulos |
| E-mail(s) |
iatropoulos@marionegri.it
|
| Organization name |
IRCCS Istituto di Ricerche Farmacologiche Mario Negri
|
| Lab |
Documentazione e Ricerca sulle Malattie Rare
|
| Street address |
Via G.B. Camozzi, 3
|
| City |
Ranica |
| State/province |
BG |
| ZIP/Postal code |
24020 |
| Country |
Italy |
| |
|
| Platform ID |
GPL17301 |
| Series (1) |
| GSE56625 |
Direct reprogramming of human mesenchymal stem cells into functional renal cells using cell-free extracts |
|
| Relations |
| BioSample |
SAMN02724802 |
| SRA |
SRX514576 |
