|
| Status |
Public on Jun 26, 2015 |
| Title |
MSC_CTRL_rp1 |
| Sample type |
SRA |
| |
|
| Source name |
MSC
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: MSC
treatment: control
tissue: Bone marrow
|
| Treatment protocol |
MSCs were starved overnight in serum free medium and treated for 1 hour with recombinant human TGFα (PeproTech,Rocky Hill, NJ, USA) at a concentration of 10 ng/ml.
|
| Growth protocol |
Bone marrow-derived MSCs were purchased from Lonza (Verviers, Belgium) and maintained in MSCGM bullet kit (Lonza) in a humidified atmosphere at 37 °C and 5% CO2, as suggested by the provider.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from untreated or TGFα-treated MSCs using TRIReagent, according to the manufacturer’s protocol (Ambion/Life Technologies, Milan, Italy). Poly(A) RNA was isolated using the Ambion MicroPoly(A) Purist Kit (LifeTechnologies).
RNA libraries were prepared for sequencing using standard Applied Biosystems SOLiD 5500xl protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
AB 5500xl Genetic Analyzer |
| |
|
| Data processing |
Whole-transcriptome reads were aligned to the version 19 of the human genome (hg19) with the SOLiD LifeScope Genomic Analysis Software version 2.5 (Life Technologies) using the parameters recommended in the user’s manual.
The automatic quantification of transcriptional events across the entire genome was performed with LifeScope.
The number of observed counts (number of reads/gene) was normalized for the length of the transcript and the number of mapped reads (RPKM) (Reads Per Kilobase per Million of mapped reads).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample
|
| |
|
| Submission date |
Aug 20, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Nicola Normanno |
| Organization name |
INT PASCALE
|
| Street address |
via Mariano Semmola
|
| City |
Naples |
| ZIP/Postal code |
80138 |
| Country |
Italy |
| |
|
| Platform ID |
GPL16288 |
| Series (1) |
| GSE60560 |
RNA-seq analysis reveals significant effects of EGFR signaling on mesenchymal stem cells (MSC) |
|
| Relations |
| BioSample |
SAMN02999577 |
| SRA |
SRX683756 |
