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| Status |
Public on Oct 01, 2023 |
| Title |
OP3 RNAseq |
| Sample type |
SRA |
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| Source name |
paracancerous tissue of oral cavity carcinomas
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| Organism |
Homo sapiens |
| Characteristics |
tissue: oral mucosa
tissue: paracancerous tissue of oral cavity carcinomas
disease state: high and middle differentiated
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| Extracted molecule |
total RNA |
| Extraction protocol |
Tissues were frozen on dry ice, and RNA was harvested using Trizol reagent.
After the total RNA was extracted from the sample, the ribosomal RNA was removed to retain all coding RNA and ncRNA. The obtained RNA was randomly broken into short fragments, and then the first strand of cDNA was synthesized with six base random primers using the fragmented RNA as the template; Then, buffer, dNTPs (dUTP instead of dTTP), RNase H and DNA polymerase I were added to synthesize the second strand of cDNA, which was purified by QiaQuick PCR kit and eluted with EB buffer, repaired at the end, added base A and adapter, and then degraded the second strand by UNG (Uracil-N-Glycosylase) enzyme. Agarose gel electrophoresis was used for fragment size selection and PCR amplification.
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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 Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to reference genome using HISAT2(2.1.0)
FPKM were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: Homo sapiens ensemb release101
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
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| Submission date |
Oct 04, 2021 |
| Last update date |
Oct 01, 2023 |
| Contact name |
Can Wei |
| E-mail(s) |
canwei528@126.com
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| Organization name |
Harbin Medical University
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| Department |
Department of Pathophysiology
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| Street address |
Baojian Road
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| City |
Harbin |
| ZIP/Postal code |
150081 |
| Country |
China |
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| Platform ID |
GPL20301 |
| Series (2) |
| GSE185249 |
Translatomics coupled with transcriptomics reveals a novel mechanism of oral carcinogenesis [RNA-seq] |
| GSE185250 |
Translatomics coupled with transcriptomics reveals a novel mechanism of oral carcinogenesis |
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| Relations |
| BioSample |
SAMN22039031 |
| SRA |
SRX12476674 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5608773_OP3.txt.gz |
95.7 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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