|
| Status |
Public on Mar 28, 2019 |
| Title |
MC3T3_NC |
| Sample type |
SRA |
| |
|
| Source name |
osteoblast
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57B6J
cell line: MC3T3
cell type: osteoblast
genotype: control
|
| Treatment protocol |
To induce Mouse and human BMSCs differentiation, the medium was completely replaced with osteogenic differentiation medium containing 10 nM dexamethasone (Sigma-Aldrich, USA), 50 μg/ml ascorbic acid and 5 mM β-glycerophosphate. The differentiation medium was changed every 2 d and cells were harvested after two weeks. KI mice osteoblasts seeded in 6-well plates were transient transfected with lnc-ob1 ASO using Lipofectamine 3000 reagent (Life Technologies) and harvested after 48 h.
|
| Growth protocol |
Mouse and human BMSCs were seeded in T25 culture flasks, and osteogenic differentiation was induced when the cells reached approximately 90% confluence. MC3T3 cells seeded in 6-well plates were transient transfected with lnc-ob1 ASO using Lipofectamine 3000 reagent (Life Technologies) and harvested after 48 h.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
After the cells were harvested, total RNA was isolated from the cells using Trizol reagent (Life Technologies).
Before constructing total RNA libraries, rRNA of the samples were removed via a method Selective Depletion of abundant RNA (SDRNA) which described by Morlan, J.D. (Morlan, J.D. et al. Plos One, 2012). Subsequently, RNA libraries were prepared for next-generation sequencing according to the protocol of VAHTS mRNA-seq v2 Library Prep Kit for Illumina while without isolated poly (A)+ RNA transcripts. The poly (A)+ RNA libraries of lnc-OB1 knockdown KI mice and N.C control KI mice were prepared according to the protocol of VAHTS mRNA-seq v2 Library Prep Kit for Illumina.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Data processing |
Illumina bcl2fastq2-v2.17 software used for basecalling.
After filtered out less than 50 bp reads with raw reads trimming adapter, the reads of hBMSC and mBMSC sample were mapped to transcript reference libraries Ensemble Homo sapiens GRCh38 and Ensemble Mus musculus GRCm38 with FANSe3 with parameters -L150 -S12 -E8p -U0. The reads of lnc-OB1_ASO and NC samples were mapped to transcript reference libraries refseq Mus musculus GRCm38 with the same parameteres.
Gene expression levels are quantified using RPKM (reads per kilobase per million reads) as unit.
Genome_build: Homo sapiens GRCh38 and Ensemble Mus musculus GRCm38
Supplementary_files_format_and_content: tab-delimited text files include read counts and RPKM values for each Sample.
|
| |
|
| Submission date |
Mar 26, 2018 |
| Last update date |
Mar 28, 2019 |
| Contact name |
Gong Zhang |
| E-mail(s) |
zhanggong@jnu.edu.cn
|
| Organization name |
Jinan University
|
| Department |
Institute of Life and Health Engineering
|
| Lab |
Translatomics Lab
|
| Street address |
Huang-Pu Avenue West 601
|
| City |
Guangzhou |
| ZIP/Postal code |
510632 |
| Country |
China |
| |
|
| Platform ID |
GPL21273 |
| Series (1) |
| GSE112318 |
The long noncoding RNA lnc-ob1 facilitates bone formation by upregulating Osterix in osteoblasts |
|
| Relations |
| BioSample |
SAMN08794867 |
| SRA |
SRX3845772 |
