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| Status |
Public on Dec 15, 2021 |
| Title |
Japanese nasal polyp 3 |
| Sample type |
SRA |
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| Source name |
Nasal polyp
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| Organism |
Homo sapiens |
| Characteristics |
disease state: Japanese chronic rhinosinusitis with nasal polyp
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| Extracted molecule |
total RNA |
| Extraction protocol |
Nasal polyp tissues from CRSwNP, and uncinate process tissues from control patients, were collected, placed in RNALater solution (Ambion, Austin, TX). RNA was extracted using NucleoSpin RNA (Macherey-Nagel, Duren, Germany). RNA-seq libraries were constructed using NEBNext Ultra II RNA Library Prep Kit for Illumina (New England BioLabs, Beverly, MA).
RNA libraries were prepared for sequencing using standard protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
readcount_genename.txt
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| Data processing |
Base calling performed using CASAVA base recognition.
RAW data are stored in FASTQ format files and filtered by removing reads with adaptor contamination, reads when certain nucleotides constitute more than 10 percent of either read, and reads when low quality nucleotides constitute more than 50 percent of the read.
Indexes of the reference genome was built using STAR and paired-end clean reads were aligned to the reference genome using STAR (v2.5).
HTSeq v0.6.1 was used to count the read numbers mapped of each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
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| Submission date |
Jul 01, 2021 |
| Last update date |
Dec 15, 2021 |
| Contact name |
Tsuguhisa Nakayama |
| Organization name |
Stanford University
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| Department |
Department of Otolaryngology-Head and Neck Surgery
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| Street address |
801 Welch Road
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| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
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| Platform ID |
GPL24676 |
| Series (2) |
| GSE179265 |
Inflammatory molecular endotypes of nasal polyps derived from Caucasian and Japanese populations |
| GSE179269 |
Inflammatory molecular endotypes of nasal polyps derived from Caucasian and Japanese populations |
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| Relations |
| BioSample |
SAMN19990305 |
| SRA |
SRX11326767 |
| 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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