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Sample GSM5412756 Query DataSets for GSM5412756
Status Public on Dec 15, 2021
Title Japanese nasal polyp 5
Sample type SRA
Source name Nasal polyp
Organism Homo sapiens
Characteristics disease state: Japanese chronic rhinosinusitis with nasal polyp
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
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
Description readcount_genename.txt
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
Submission date Jul 01, 2021
Last update date Dec 15, 2021
Contact name Tsuguhisa Nakayama
Organization name Stanford University
Department Department of Otolaryngology-Head and Neck Surgery
Street address 801 Welch Road
City Stanford
State/province CA
ZIP/Postal code 94305
Country USA
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
BioSample SAMN19990303
SRA SRX11326769

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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