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| Status |
Public on Nov 27, 2019 |
| Title |
mirna_4 |
| Sample type |
SRA |
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| Source name |
Nasopharyngeal carcinoma biopsy
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| Organism |
Homo sapiens |
| Characteristics |
tissue: nasopharyngeal carcinoma
disease status: NPC
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from NPC specimens and normal nasopharyngeal mucosal specimens using TRIzol reagent (Invitrogen; Carlsbad, CA, USA). The RNA concentration was measured with a NanoDrop2000 Spectrophotometer (NanoDrop Technologies; Wilmington, DE, USA), and the integrity of purified RNA was determined using Agilent 2100 Bioanalyzer (Agilent Technologies; Palo Alto, CA USA). miRNA quantification was evaluated using Hot Start PCR.
A small RNA library was built using the Next Multiplex Small RNA Library Prep Set for Illumina (NEB; Ipswich, MA, USA) according to the manufacturer’s protocol. Polyacrylamide gel electrophoresis was performed to purify small RNA and to enrich for molecules ranging from 18 to 30 nt. Then, cDNA was synthesized, digested and amplified to set cDNA libraries, followed by purification on a polyacrylamide gel and quantification.
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| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 4000 |
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| Data processing |
Sequencing data were aligned to the reference human genome (UCSC hg19) and EBV genome (GCF_000872045.1).
Reads mapped to known miRNAs were identified by searching miRBase database (v21). Novel miRNAs were predicted by miRDeep. Known and novel miRNA expression levels were measured by the number of mapped reads.
Genome_build: hg19
Supplementary_files_format_and_content: text file with raw read count
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| Submission date |
Aug 17, 2018 |
| Last update date |
Nov 27, 2019 |
| Contact name |
Bin Zhang |
| Organization name |
Icahn School of Medicine at Mount Sinai
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| Department |
Genetics and Genomic Sciences
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| Street address |
1470 Madison Avenue
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| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10029 |
| Country |
USA |
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| Platform ID |
GPL20301 |
| Series (2) |
| GSE118720 |
miRNA-Seq profiling of nasopharyngeal carcinoma (NPC) and normal control samples |
| GSE118721 |
Transcriptomic profiling of mRNA and miRNA from nasopharyngeal carcinoma (NPC) and normal control samples |
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| Relations |
| BioSample |
SAMN09848877 |
| SRA |
SRX4565020 |
| 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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