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| Status |
Public on Feb 15, 2023 |
| Title |
S4-N, adjacent normal tissues (RNA-seq) |
| Sample type |
SRA |
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| Source name |
adjacent normal tissues
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| Organism |
Homo sapiens |
| Characteristics |
tissue: adjacent normal tissues
pair id: S4-N
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| Extracted molecule |
total RNA |
| Extraction protocol |
Frozen tissues were extracted using the QIAamp Fast DNA Tissue Kit (Qiagen) for DNA.The experimental process was performed according to the standard protocol provided by Oxford Nanopore Technologies (ONT), including sample quality detection, library construction, library quality detection and library sequencing.
DNA-seq libraries were captured to exome regions using Roche NimbleGen SeqCap EZ Exome V3/Agilent SureSelect Human All Exon V6. RNA was subjected to library preparation using ONT Direct RNA Sequencing Kit. Libraries were sequenced on PromethION.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
PromethION |
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| Description |
All_gene_expression.list
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| Data processing |
For sequencing data, FASTQ files were generated by CASAVA 2.0. The human reference file that was used is GRCh37/hg19.Duplicates were removed using Picard. The base quality scores were recalibrated using BaseRecalibrator (GATK). Single nucleotide variations (SNVs) were identified using MuTect. Somatic indels of tumor–normal pairs were called using GATK Somatic Indel Detector. Variants annotations were obtained using the software tool ANNOVAR.
The full-length sequenced transcriptome was used as a reference for sequence alignment and subsequent analysis, and minimap2 was used to align the clean reads with the reference transcriptome to obtain the corresponding information of the transcript and the reference transcriptome.
Assembly: mm10
Supplementary files format and content: WES: tab-delimited text files include indel and snp
Supplementary files format and content: RNA-seq: tab-delimited text files include RPKM values for each Sample
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| Submission date |
Dec 01, 2022 |
| Last update date |
Feb 15, 2023 |
| Contact name |
Yuchuan Wang |
| E-mail(s) |
[email protected]
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| Organization name |
Tianjin Eye hospital
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| Street address |
Gansu Road
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| City |
Tianjin |
| ZIP/Postal code |
300020 |
| Country |
China |
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| Platform ID |
GPL26167 |
| Series (1) |
| GSE219205 |
Integrated whole-exome and transcriptome sequencing indicated dysregulation of cholesterol metabolism in eyelid sebaceous gland carcinoma |
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| Relations |
| BioSample |
SAMN31978669 |
| SRA |
SRX18458521 |
| 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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