|
| Status |
Public on Nov 05, 2021 |
| Title |
Chondrocytes, IL-1β (circRNA-Seq) |
| Sample type |
SRA |
| |
|
| Source name |
chondrocytes
|
| Organism |
Rattus norvegicus |
| Characteristics |
cell type: chondrocytes
Sex: male
age: 6-day-old
treatment: IL-1β treated
|
| Treatment protocol |
Chondrocytes within P3 generation were used in this study.Rat chondrocytes were treated with recombinant rat IL-1β (cat. No. I2393; Sigma Aldrich; 10 ng/ml) for 24 h to establish an in vitro OA cellular model as previously described (Huang et al., 2019). Chondrocytes cultured under normal conditions without IL-1β were set as normal control (NC) group.
|
| Growth protocol |
Cell was cultured in GIBCO DMEM/F12 (1:1) medium (No.: C11330500BT), supplemented with 10% fetal bovine plasma (FBS; Gibco) and 1% penicillin and streptomycin (Sigma Aldrich).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Briefly, total RNA samples were extracted from chondrocytes after the indicated treatments. The RNA integrity was evaluated using an Agilent 2100 Bioanalyzer. The fragment size of RNA was determined by agarose gel electrophoresis. The rRNA components were removed from the RNA samples using the Qiagen RiboMinus Eukaryote Kit, according to the manufacturer’s instructions.
The RNA library for sequencing was established from the mixed RNA samples (from three independent experiments) using the NEBNext Ultra II RNA Library Prep Kit (#E7770S; NEB, United States) according to the protocol provided by the manufacturer. Finally, the constructed RNA library was sequenced using a Hiseq 2000 instrument (Illumina,United States).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
one sample from chondrocytes of male rat
|
| Data processing |
fastqc do QC
Sequenced reads were filter by SOAPnuke1.4.1(-f AGATCGGAAGAGC -r AGATCGGAAGAGC -A 0.62 -l 5 -q 0.25 -Q 2)
fastqc do cleandata QC
bwa-0.7.12 Compare to the reference genome ;CIRI_v2.0.5 get circ sequence
Transcripts Per Kilobase of exon model per Million mapped reads(TPM)
Genome_build: rn6
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample
|
| |
|
| Submission date |
Nov 02, 2021 |
| Last update date |
Nov 06, 2021 |
| Contact name |
li hao yuan |
| E-mail(s) |
lihaoyuan@forevergen.cn
|
| Organization name |
Forevergen Biosciences Co.,Ltd
|
| Street address |
International Biotech Island
|
| City |
Guangzhou |
| ZIP/Postal code |
510000 |
| Country |
China |
| |
|
| Platform ID |
GPL14844 |
| Series (2) |
| GSE186992 |
CircPan3 Promotes the Ghrelin System and Chondrocyte Autophagy by Sponging miR-667-5p During Rat Osteoarthritis Pathogenesis [circRNA-Seq] |
| GSE186993 |
CircPan3 Promotes the Ghrelin System and Chondrocyte Autophagy by Sponging miR-667-5p During Rat Osteoarthritis Pathogenesis |
|
| Relations |
| BioSample |
SAMN22837253 |
| SRA |
SRX12895250 |
