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| Status |
Public on Jul 01, 2023 |
| Title |
Emodin1 |
| Sample type |
SRA |
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| Source name |
Fibroblast-like synoviocytes
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| Organism |
Rattus norvegicus |
| Characteristics |
disease state: rheumatoid arthritis
cell type: Fibroblast-like synoviocytes
genotype: WT
treatment: TNF-a + emodin
time: Day 5
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| Treatment protocol |
Fresh medium was used to replace the culture medium every 2 days. When the confluence of cells reached 85%, trypsin digestion and passage to the 4th generation at a ratio of 1:3 for follow-up experiments. Two experimental groups were used in the current study, namely the TNF-α group (cells were administered with TNF-α at a concentration of 10 ng/ml), and EMO group (co- administered with 80 μmol/L EMO and 10 ng/ml TNF-α)
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| Growth protocol |
Fibroblast-like synoviocytes cells were inoculated in DMEM medium containing high level of glucose medium supplemented with FBS (15%), and antibiotics (100U/ml penicillin, and 100 μg/ml streptomycin). A cell culture incubator (Sanyo, Japan) was used to culture the cells at 5% CO2 and 37°C.
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| Extracted molecule |
total RNA |
| Extraction protocol |
The Qiagen RNeasy Kit (Cat#74106, USA) was used to isolate and purify total RNAs. The quality of RNA samples was determined using Nanodrop (Thermo Fisher Scientific). An Agilent 2100 Bioanalyzer was used to evaluate the results.
In Novogene (China), RNA libraries were prepared, and data was processed. Next, 1μg of RNA was utilized for each sample, followed by generating libraries using Illumina NEBNext UltraTM RNALibrary Prep Kit (NEB, USA), as suggested by the manufacturer. The first step was to purify mRNA by binding polyA to mRNA using OligodT-labeled magnetic beads (llumina Inc., San Diego, USA). The mRNA was then mixed with NEBNext First Strand Synthesis Reaction Buffer (5X). A short fragment of 200-300 bp in size was obtained by mixing. MMuLV Reverse Transcriptase without RNase H activity and random hexamer primers were used to generate first-strand cDNA. Conversion of this cDNA to double-stranded cDNA using RnaseH and DNA Polymerase I. Under the function of 3'-5' exonuclease and polymerase, fragmentation overhangs were translated to blunt ends. DNA fragments were adenylated, and the fragments were then ligated to the sequencing adapter by A and T complementary base pairing. Then, sequencing libraries were constructed using the AMPure XP system purification method (Beckman Coulter, Shanghai, China) and PCR methods.Finally, the libraries were evaluated by the Agilent Bioanalyzer 2100 system. Poly(A) selected paired-end sequencing libraries were generated according to the instructions in the TruSeq manual. The sequencer Illumina HiSeq 2000 was emploved to sequence all the libraries.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
D_1
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| Data processing |
Perform quality analysis on acquired fastq sequence files using fastQC software. Use Trimmomatic software to remove adapters and make appropriate modifications to base pairs, trim base pairs, and filter low-quality sequences.
Use hisat2 software to align fasta sequences to a reference genome. First, build an index file by downloading or copying the reference genome sequence file Ref and genome annotation file and using the hisat2-build command.
Assembly: Rnor_6.0
Supplementary files format and content: tab-delimited text files include count values for all Samples
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| Submission date |
May 17, 2023 |
| Last update date |
Jul 01, 2023 |
| Contact name |
chunhao cao |
| E-mail(s) |
CHUNHAO@hkbu.edu.hk
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| Organization name |
Hong Kong Baptist University
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| Department |
School of Chinese Medicine
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| Street address |
Hong Kong
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| City |
Hong Kong |
| ZIP/Postal code |
999077 |
| Country |
Hong Kong |
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| Platform ID |
GPL18694 |
| Series (1) |
| GSE232679 |
The elucidation of the anti-inflammatory mechanism of EMO in rheumatoid arthritis through an integrative approach combining bioinformatics and experimental verification |
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| Relations |
| BioSample |
SAMN35130737 |
| SRA |
SRX20388982 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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