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| Status |
Public on Mar 01, 2024 |
| Title |
p38.S069.day23 |
| Sample type |
SRA |
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| Source name |
blood
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| Organism |
Homo sapiens |
| Characteristics |
tissue: blood
patient: 38
Sex: F
condition: SLE
responder: NR
time point: day23
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extraction was carried out using Thermo Fisher's MagMAX™ kit, specifically designed for PAXgene™ Blood RNA Tubes. Subsequently, sample quality control was conducted using the Agilent 2100 bioanalyzer, with a threshold set at RIN>7 to identify suitable samples. Qualified RNA from each sample was then subjected to non-stranded mRNAseq library preparation, which included globin depletion.
The library preparation process involved mRNA fragmentation, followed by the generation of first-strand cDNA using random hexamer-primed reverse transcription. This was followed by second-strand cDNA synthesis and adapter ligation reactions. The resulting libraries were PCR-enriched and purified using Ampure XP beads, with library quantification performed using the Agilent Technologies 2100 bioanalyzer. The subsequent steps included heat denaturation and circularization of double-stranded PCR products, leading to the formation of single-strand circular DNA (ssCir DNA) libraries. These libraries were then amplified with phi29 to create DNA nanoballs (DNBs), each containing more than 300 copies of a single molecular entity. These DNBs were loaded onto a patterned nanoarray, and sequencing was carried out to generate paired-end 150 base reads through sequenced by synthesis using the DNBSEQ-G400 platform.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
DNBSEQ-G400 |
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| Description |
S069
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| Data processing |
We used Trim Galore (v0.6.5) to trim Illumina adaptors from the raw fastq reads and removed reads that were too short after adaptor trimming (less than 20 nt). We then used Salmon (v1.2.1) to get transcript-level expression based on human transcriptome sequences from GENCODE site (v32). Gene-level expression was summarized using Tximport (v1.16.0).
Assembly: GRCh38
Supplementary files format and content: readcount.csv.gz: read count from Salmon; samplemeta.csv: sample meta data
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| Submission date |
Dec 12, 2023 |
| Last update date |
Mar 01, 2024 |
| Contact name |
Hong Zheng |
| Organization name |
Stanford university
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| Street address |
240 Pasteur Dr
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| City |
Stanford |
| State/province |
California |
| ZIP/Postal code |
94304 |
| Country |
USA |
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| Platform ID |
GPL28038 |
| Series (2) |
| GSE250023 |
Impaired innate and adaptive immune responses to BNT162b2 SARS-CoV-2 vaccination in systemic lupus erythematosus |
| GSE250025 |
Impaired innate and adaptive immune responses to BNT162b2 SARS-CoV-2 vaccination in systemic lupus erythematosus |
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| Relations |
| BioSample |
SAMN38792946 |
| SRA |
SRX22870866 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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