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| Status |
Public on Mar 09, 2023 |
| Title |
SALM_1 |
| Sample type |
SRA |
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| Source name |
salivary adenoid cystic carcinoma
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| Organism |
Homo sapiens |
| Characteristics |
tissue: salivary adenoid cystic carcinoma
treatment: DMSO
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extracted from 1×10^7 cells in 1 mL TRIZOL reagen
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
DNBSEQ-G50 |
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| Data processing |
A total of 18 samples were tested using the DNBSEQ platform, with an average yield of 1.19G data per sample. The average alignment ratio of the sample comparison genome was 94.90%, which was comparative The average alignment of the gene set was 80.35%; a total of 18782 genes were detected.
Reference Genome Version：GCF_000001405.39_GRCh38.p13
The raw data for sequencing contains reads of low quality, adaptor contamination, and excessively high levels of unknown base N. These reads need to be removed before data analysis to ensure the reliability of the results. For the quality index of filtered reads, see the filtered reads quality statistics table and the raw data filtering component statistics chart. For the base content distribution and quality distribution, see the base content distribution chart of clean reads and the base quality distribution chart of clean reads.
After getting clean reads, we used HISAT to align the clean reads to the reference genome. The alignment results are shown as follows.Align clean reads to the reference genes by using Bowtie2 to get the alignment result.
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| Submission date |
Nov 02, 2022 |
| Last update date |
Mar 09, 2023 |
| Contact name |
kong lu |
| E-mail(s) |
konglu@ccmu.edu.cn
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| Organization name |
ccmu
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| Street address |
capital medical university
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| City |
peking |
| ZIP/Postal code |
100086 |
| Country |
China |
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| Platform ID |
GPL28337 |
| Series (2) |
| GSE216852 |
Increased retinoic acid signalling decreases lung metastasis in salivary adenoid cystic carcinoma by inhibiting the noncanonical Notch1 pathway |
| GSE217083 |
Increased retinoic acid signalling decreases lung metastasis in salivary adenoid cystic carcinoma by inhibiting the noncanonical Notch1 pathway [RNA-seq_treated] |
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| Relations |
| BioSample |
SAMN31572068 |
| SRA |
SRX18120389 |
| 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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