|
| Status |
Public on Nov 26, 2020 |
| Title |
rBMSCs, M-CS-3 |
| Sample type |
SRA |
| |
|
| Source name |
Bone marrow mesenchymal stem cells
|
| Organism |
Oryctolagus cuniculus |
| Characteristics |
breed: New Zealand white
treatment: cultured on Calcium Silicate scaffolds treated with Medium
age: post natal day 8 weeks
cell type: Rabbit bone marrow mesenchymal stem cells (rBMSCs)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
rBMSCs grown on scaffolds were collected by trypsin enzyme digesting technique, and RNA was then harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: OryCun2.0 (GCF_000003625.3)
Supplementary_files_format_and_content: tab-delimited text file includes counts and FPKM values for each Sample
|
| |
|
| Submission date |
Nov 25, 2020 |
| Last update date |
Nov 26, 2020 |
| Contact name |
Mengmeng Li |
| E-mail(s) |
limengmeng@mail.sic.ac.cn
|
| Organization name |
Shanghai Institute of Ceramics, Chinese Academy of Sciences
|
| Street address |
1295 Dingxi Road
|
| City |
Shanghai |
| ZIP/Postal code |
200050 |
| Country |
China |
| |
|
| Platform ID |
GPL26786 |
| Series (1) |
| GSE162127 |
RNA-Seq analysis used to explore the bone-froming mechanism of microbially catalyzed biomaterials |
|
| Relations |
| BioSample |
SAMN16911807 |
| SRA |
SRX9573101 |
