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Sample GSM4734673

Query DataSets for GSM4734673

Status

Public on Aug 22, 2020

Title

A549 circNDUFB2 rep2

Sample type

SRA

Source name

A549 cells

Organism

Homo sapiens

Characteristics

tissue: lung
cell line: A549

Extracted molecule

total RNA

Extraction protocol

A549 cells were washed by PBS, and RNA was harvested using Trizol reagent. 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 HiSeq 2000

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 hg38 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: hg38
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

Aug 21, 2020

Last update date

Aug 22, 2020

Contact name

Botai Li

E-mail(s)

libotai@zju.edu.cn

Phone

15221287275

Organization name

Botai Li