|
| Status |
Public on Sep 18, 2022 |
| Title |
MJ rep3 |
| Sample type |
SRA |
| |
|
| Source name |
macrophage
|
| Organism |
Mus musculus |
| Characteristics |
strain: BALB/c
tissue: Blood lymph
passages: 30
|
| Treatment protocol |
RANKL (50 ng/mL), heat-killed P. freudenreichii MJ2 (1 x 10^7 cells/mL), and surface protein extracted from P. frudenreichii MJ2 (10 μg/mL) were treated for 4 days.
|
| Growth protocol |
Raw 264.7 cells were seeded at the concentration of 1 x 10^5 cells/mL on 6-mm dish and incubated in DMEM containing 10% fetal bovine serum and 1% penicillin and streptomycin at 37℃ with the atmosphere of 5% CO₂ for overnight.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to mm10 (UCSC) whole genome using Bowtie2
Read count extraction using bedtools.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include read count values for each Sample
|
| |
|
| Submission date |
Sep 11, 2022 |
| Last update date |
Sep 19, 2022 |
| Contact name |
jiah yeom |
| E-mail(s) |
[email protected]
|
| Organization name |
Korea university
|
| Street address |
Anamro 145
|
| City |
seoul |
| ZIP/Postal code |
02841 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE213113 |
Propionibacterium freudenreichii MJ2 inhibits RANKL-induced osteoclast differentiation and ameliorates rheumatoid arthritis in collagen-induced arthritis model |
|
| Relations |
| BioSample |
SAMN30797811 |
| SRA |
SRX17527393 |
