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Sample GSM7915824

Query DataSets for GSM7915824

Status

Public on Mar 28, 2024

Title

Healthy control [DK22269_14]

Sample type

SRA

Source name

PBMC

Organism

Homo sapiens

Characteristics

disease: Healthy
tissue: PBMC
age: 71
Sex: Male
race: Asian
treatment: None

Extracted molecule

total RNA

Extraction protocol

RNA was harvested using ISOGEN reagent (Life Technologies, Carlsbad, CA, USA).
Purified total RNA (200 ng) was used for RNA library preparation, according to the instructions of the Quant Seq 3' mRNA-seq library preparation kit FWD of Illumina (Lexogen, Vienna, Austria). The RNA libraries were sequenced on an Illumina NextSeq 500 system with 75-nt-long reads.

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina NextSeq 500

Description

DK22269_14
3' RNA-seq

Data processing

Removal of poly A tail and adapter sequences were performed using BBDuk (BBMap version 38.96) with the following settings (k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20).
Trimmed reads were mapped to hg38 using STAR version 2.7.6a with the following settings (--outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.1 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000).
Read counts for each gene were obtained using HTSeq-count version 1.99.2 with the following settings (-m intersection-nonempty -s yes).
Assembly: hg38
Supplementary files format and content: xlsx files include raw counts for each sample.
Supplementary files format and content: xlsx files include RPM values for each sample.

Submission date

Nov 22, 2023

Last update date

Mar 28, 2024

Contact name

Takeshi Kawasaki

E-mail(s)

kawatake@chiba-u.jp

Phone

+81-43-222-7171

Organization name

Chiba University