|
| Status |
Public on Aug 25, 2017 |
| Title |
Ptpn11++MSPC |
| Sample type |
SRA |
| |
|
| Source name |
Mesenchymal stem/progenitor cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: BM derived Mesenchymal stem/progenitor cells
genotype: Ptpn11+/+
|
| Extracted molecule |
total RNA |
| Extraction protocol |
MSPCs (CD45-Ter-119-CD31-CD140+Sca-1+) were freshly isolated from the BM of Ptpn11E76K/+/Nestin-Cre+ and Ptpn11+/+/Nestin-Cre+ mice
RNA was extracted using the Rneasy Midi kit (Qiagen). Total RNA samples were enriched for polyadenylated transcripts using the Oligotex mRNA Mini kit (Qiagen)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Raw image data file from high-throughput sequencing(like Illumina HiSeqTM2500/MiseqTM) was transformed to Sequenced Reads(called Raw Data or Raw Reads) by CASAVA base recognition (Base Calling, version 1.4).
Raw Data is stored in FASTQ(fq) format files, which contain reads sequence and corresponding base quality
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using Tophat Version V2.0.9
For each sequenced library, the read counts were adjusted by edgeR program package through one scaling normalized factor.
Genome_build: mm9
Supplementary_files_format_and_content: read count
|
| |
|
| Submission date |
May 11, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
LEI Dong |
| E-mail(s) |
lei.dong@emory.edu
|
| Organization name |
Emory University
|
| Street address |
1760 Haygood Drive NE, HSRB E3642
|
| City |
Atlanta |
| ZIP/Postal code |
30322 |
| Country |
USA |
| |
|
| Platform ID |
GPL21103 |
| Series (1) |
| GSE81311 |
Murine mesenchymal stem/progenitor cells (MSPC): Ptpn11+/+ MSPC vs. Ptpn11E76K/+ MSPC |
|
| Relations |
| BioSample |
SAMN04978512 |
| SRA |
SRX1756410 |
