|
| Status |
Public on Jun 25, 2013 |
| Title |
mock-DM+BMP2 |
| Sample type |
SRA |
| |
|
| Source name |
BMP2-treated mock-transfected C2C12 cells
|
| Organism |
Mus musculus |
| Characteristics |
cell line: C2C12 mesenchymal precursor cell line
genotype/variation: control
agent: BMP2
|
| Treatment protocol |
Myogenic differentiation of C2C12 cells was induced by incubation in DMEM plus 2% horse serum (Differentiation Medium, DM). Osteoblastic differentiation of C2C12 cells was induced by the addition of 100-300 ng/ml of recombinant BMP2 (R&D Systems, Minneapolis, MN).
|
| Growth protocol |
Murine mesenchimal C2C12 cells (obtained from ATCC, no. CRL-1772, Lot no. 58236521) were cultured in DMEM plus 20% FBS (Growth Medium, GM).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The RNA-Seq library was generated from total RNA prepared using miRNeasy (Qiagen, Milan, I) and purified twice with Sera-mag Magnetic Oligo(dT) Beads (Thermo Fisher, Waltham, MA) according to Illumina’s sample preparation instruction at LC-Sciences (Houston, TX). ). Purified mRNA samples were treated with a divalent cation solution followed by ethanol precipitation. Fragmented mRNAs were preceded for cDNA synthesis.
The double-stranded cDNA fragments were end-repaired and 5’ and 3’ Ligation of Illumina’s paired-end oligo adapters was performed. The library was purified on a 2% agarose gel (250±25 bps). The cDNA library was enriched by 18 cycles of PCR, gel purified, and used for cluster generation on Illumina’s Cluster Station and then sequenced on Illumina HiSeqTM 2000 following vendor’s instruction.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
C2C12_mock_1d
|
| Data processing |
basecalling Illumina RTA 1.13
CASAVA 1.8
aligner Bowtie 0.12.7
alternative splicing and differential expression: TopHat 1.4.1, CuffLinks 1.3.0
Genome_build: mm9
Supplementary_files_format_and_content: cufflink's FPKM 'transcript.gtf' file
|
| |
|
| Submission date |
Jun 25, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Gabriele Bucci |
| E-mail(s) |
bucci.gabriele@hsr.it
|
| Organization name |
Università vita e Salute Ospedale San Raffaele
|
| Department |
Center of Translational Genomics and Bioinformatics
|
| Lab |
GFU
|
| Street address |
Via Olgettina 60
|
| City |
Milan |
| ZIP/Postal code |
20132 |
| Country |
Italy |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE38907 |
KSRP-mediated Transcriptome reshaping |
|
| Relations |
| SRA |
SRX155852 |
| BioSample |
SAMN01057605 |
