|
| Status |
Public on Aug 30, 2019 |
| Title |
Akap11-KO_Day16 |
| Sample type |
SRA |
| |
|
| Source name |
MC3T3-E1
|
| Organism |
Mus musculus |
| Characteristics |
genotype: Akap11 -/-
cell line: MC3T3-E1
|
| Treatment protocol |
50 µg/ml ascorbic acid and 5 mM β-glycerophosphate were added to the medium for osteogenic differentiation. Medium was changed every 3 days and cells were incubated at 37 °C in a 5% CO2 atmosphere.
|
| Growth protocol |
Cell were maintained in proliferation medium, α‐MEM (Gibco, Thermo Fisher Scientific, Waltham, MA, USA; catalog # 12571) containing 10% v/v fetal bovine serum (FBS), 100 units/mL penicillin and 100 μg/mL streptomycin.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cell were washed with PBS and RNA was harvested using Trizol reagent.
100ng total RNA was used for library construction by KAPA Stranded mRNA-Seq Kit (Roche).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1500 |
| |
|
| Description |
D16_KOvsWT_gene_exp.diff
|
| Data processing |
Base calling was performed using Illumina’s RTA (Version 1.12.4.2).
Adapters of RNA-seq reads were trimmed.
The BAM files with coordinate-sorted alignments were imported to Cufflinks 2.2.1 to assemble and quantify the transcripts as fragments per kilobase per million aligned reads (FPKM).
Cuffdiff 2 was employed to perform differential expression analysis.
Genome_build: Genome Reference Consortium Mouse Build 38
Supplementary_files_format_and_content: tab-delimited text files include log2 foldchange value
|
| |
|
| Submission date |
Aug 29, 2019 |
| Last update date |
Aug 31, 2019 |
| Contact name |
Vincent Ka Fai Cheng |
| E-mail(s) |
u3003930@connect.hku.hk
|
| Phone |
67383950
|
| Organization name |
The University of Hong Kong
|
| Department |
Pharmacology and Pharmacy
|
| Street address |
L202 lab block 21 Sassoon road Pokfulam Hong Kong
|
| City |
Hong Kong |
| State/province |
-- select -- |
| ZIP/Postal code |
000 |
| Country |
Hong Kong |
| |
|
| Platform ID |
GPL18480 |
| Series (1) |
| GSE136591 |
Akap11 is a positive regulator of osteogenesis in mouse osteoblastic cell line MC3T3-E1 |
|
| Relations |
| BioSample |
SAMN12651292 |
| SRA |
SRX6777946 |
