|
| Status |
Public on Sep 20, 2021 |
| Title |
MC3T3_3D_shLacZ_Rep1 |
| Sample type |
SRA |
| |
|
| Source name |
MC3T3-E1
|
| Organism |
Mus musculus |
| Characteristics |
cell line: Osteocyte-like cell line
genotype: 3D
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were collected and total RNA was isolated using QIAshredder (QIAGEN) and PureLink RNA Mini Kit (Invitrogen).
mRNAs were isolated by PAGE, followed by adaptor ligation and RT with PCR amplification. PCR products were again purified by PAGE and dissolved in EB solution. Double stranded PCR products were heat denatured and circularized by the splint oligo sequence. The ssCir DNA was formatted as the final sequencing library. The library was amplified with phi29 to general DNA nanoballs (DNBs) which were loaded into the patterned nanoarray. Libraries were sequenced on the BGISEQ500 platform.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
BGISEQ-500 |
| |
|
| Data processing |
Sequenced libraries were evaluated with FastQC.
Sequencing reads were mapped to the mouse reference genome (mm10) using STAR v.2.7.2b.
Gene expression counts were calculated using HTSeq v.0.9.1.
Differential expression analysis was performed using EgdeR package based on the criteria of more than two-fold change in expression value versus control and false discovery rates (FDR) <0.05.
Genome_build: mm10
Supplementary_files_format_and_content: txt files include read counts for each sample
|
| |
|
| Submission date |
Jul 21, 2021 |
| Last update date |
Sep 21, 2021 |
| Contact name |
Jialiang Wang |
| E-mail(s) |
jialiang.wang@utsouthwestern.edu
|
| Organization name |
University of Texas Southwestern Medical Center
|
| Street address |
5323 Harry Hines Blvd
|
| City |
Dallas |
| State/province |
TX |
| ZIP/Postal code |
75390 |
| Country |
USA |
| |
|
| Platform ID |
GPL23479 |
| Series (2) |
| GSE154717 |
Control of osteocyte dendrite formation by Sp7 and its target gene osteocrin [RNA-Seq] |
| GSE154719 |
Control of osteocyte dendrite formation by Sp7 and its target gene osteocrin |
|
| Relations |
| BioSample |
SAMN20342755 |
| SRA |
SRX11515756 |
