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Sample GSM5077589

Query DataSets for GSM5077589

Status

Public on May 19, 2021

Title

HC1

Sample type

SRA

Source name

Blood

Organism

Homo sapiens

Characteristics

disease: healthy control
agent: none
tissue: blood
age: post 20 years old

Extracted molecule

total RNA

Extraction protocol

Retinas were removed, flash frozen on dry ice, and RNA was harvested using BD RNA tube. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina NovaSeq 6000

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 mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) 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: mm9
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

Submission date

Feb 12, 2021

Last update date

May 19, 2021

Contact name

Han Jiang

E-mail(s)

m201875021@hust.edu.cn

Phone

18827062911

Organization name

Huazhong University of Science and Technology