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Sample GSM4317441

Query DataSets for GSM4317441

Status

Public on Feb 24, 2020

Title

OVER NRAV rep2 [NO5]

Sample type

SRA

Source name

OVER NRAV_A549

Organism

Homo sapiens

Characteristics

cell line: A549
cell type: adenocarcinoma of type II alveolar cells
passages: 6-12
genotype/variation: NIRAV overexpression

Treatment protocol

Cells were seeded in six-well plates. Plasmids or siRNAs were transfected into cells with Lipofectamine 2000 (Invitrogen) following the manufacturer’s instructions

Growth protocol

A549 cells were grown in RPMI1640 supplemented with 10% (vol/vol) FBS (Gibco) and antibiotics (penicillin and streptomycin) (Solarbio) in a humidified 5% CO2 atmosphere at 37℃.

Extracted molecule

total RNA

Extraction protocol

Total RNA was extracted using miRNeasy Mini Kit (Cat#217004, Qiagen) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US). Qualified total RNA was further purified by RNAClean XP Kit (Cat A63987, Beckman Coulter, Inc. Kraemer Boulevard Brea, CA, USA) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).
RNA libraries were prepared for sequencing using standard Illumina protocols

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 2500

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: hg38
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

Submission date

Feb 17, 2020

Last update date

Feb 25, 2020

Contact name

Jian Li

E-mail(s)

[email protected]

Organization name

Hebei Medical University

Street address

361 Zhongshan East Road