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| Status |
Public on Jul 14, 2021 |
| Title |
Synovial tisssue from Pigmented villonodular synovitis joint [zxs140421A] |
| Sample type |
SRA |
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| Source name |
Synovial tisssue from Pigmented villonodular synovitis joint
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| Organism |
Homo sapiens |
| Characteristics |
subject status: Pigmented villonodular synovitis
tissue: Synovial tisssue
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total cellular RNA of synovial tissues was isolated using a RNeasy Mini kit (Qiagen, Hilden, Germany) following the manufacturer's instructions. The concentration of each sample was measured by NanoDrop 2000 (Thermo Scientific, USA). The quality was assessed by the Agilent2200 (Agilent, USA).
The sequencing library of each RNA sample was prepared by using Ion Total RNA-Seq Kit v2 according to the protocol provided by manufacturer (Life technologies, USA). Briefly, poly(A)-containing mRNA was purified from 5 ug total RNA with Dynabeads (Life technologies, USA). The mRNA was fragmented using RNaseIII and purified. The fragmented RNA was hybrized and ligated with Ion adaptor. The RNA fragments were reverse- transcribed and amplified to double-stranded cDNA. Then, the amplified cDNA was purified by magnetic bead-based method, and the molar concentration was determined for each cDNA library.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Ion Torrent Proton |
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| Data processing |
Raw data were cleaned via fastp.
Cleaned reads were aligned to human genome (GRCh38) by hisat2.
Aligned reads were counted by Htseq.
fpkm of 6 samples were produced via DESeq2
Genome_build: GRCh38
Supplementary_files_format_and_content: raw and fpkm
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| Submission date |
Jun 04, 2021 |
| Last update date |
Jul 14, 2021 |
| Contact name |
Dai Hui |
| E-mail(s) |
[email protected]
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| Organization name |
Department of Immunology, School of Basic Medical Sciences, NHC Key Laboratory of Medical Immunology, Peking University
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| Street address |
Xue Yuan Road 28, Haidian District
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| City |
Beijing |
| ZIP/Postal code |
100191 |
| Country |
China |
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| Platform ID |
GPL17303 |
| Series (1) |
| GSE176133 |
Gene expression profiles analyzed using integrating RNA sequencing and microarray reveals increased inflammatory response, proliferation, and osteoclastogenesis in pigmented villonodular synovitis |
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| Relations |
| BioSample |
SAMN19553962 |
| SRA |
SRX11065285 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5356824_zxs140421A.txt.gz |
210.3 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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