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| Status |
Public on Jun 02, 2021 |
| Title |
FRAS190074375 |
| Sample type |
SRA |
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| Source name |
salivary glands
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| Organism |
Homo sapiens |
| Characteristics |
tissue: salivary glands
disease state: non-ILD-pSS
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from frozen salivary gland samples using TRIzol Reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions. RNA purity was checked using a Nano Photometer spectrophotometer (IMPLEN, Westlake Village, CA, USA).
The quality of the RNA used to construct the cDNA library was verified (RNA integrity numbers >9) using an RNA 6000 Nano kit with the Bioanalyzer 2100 system (Agilent Technologies, Santa Clara, CA, USA). With input material of 3 mg RNA per sample, we constructed sequencing libraries using the NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA) and subsequently performed the sequence on an Illumina HiSeq platform.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Data processing |
Illumina bcl2fastq software used for basecalling.
Using Cutadapt adapters and TrimGalore, raw reads were trimmed and low-quality reads were filtered. Quality-control reports of sequence reads were obtained using FastQC software.
The sequencing data were aligned to the human reference genome "hg38" using STAR software.
The read count files were filtered with low expression and normalized using the DESeq2 package.
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with normalized gene counts for every gene and every sample
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| Submission date |
Apr 12, 2021 |
| Last update date |
Jun 02, 2021 |
| Contact name |
Xiaofang Zhu |
| E-mail(s) |
june8587@outlook.com
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| Phone |
86+13758484680
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| Organization name |
First Affiliated Hospital of Wenzhou Medical University
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| Department |
Rheumatology
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| Street address |
Nan Bai Xiang Street
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| City |
Wenzhou |
| State/province |
Zhejiang Province |
| ZIP/Postal code |
325000 |
| Country |
China |
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| Platform ID |
GPL20301 |
| Series (1) |
| GSE171896 |
CXCR2 may serve as a useful index of disease activity in interstitial lung disease associated with primary Sjögren’s syndrome |
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| Relations |
| BioSample |
SAMN18715057 |
| SRA |
SRX10579716 |
| 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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