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Sample GSM5920729

Query DataSets for GSM5920729

Status

Public on Mar 01, 2022

Title

PR0126_15_b

Sample type

SRA

Source name

Chinese hamster ovary cells

Organism

Cricetulus griseus

Characteristics

cell line: CHO-K1 (CCL-61; ATCC)
cell type: ovary cells
treatment: clone2-medium1-day14

Extracted molecule

total RNA

Extraction protocol

Cells were removed, flash frozen on dry ice, 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 Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to chinese hamster whole genome (NW_003613580:NW_003722730) using bowtie v1.0.0 with parameters -v3 -all -m 30 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Mortazavi et al., Nature Methods, 2008. 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.
Supplementary_files_format_and_content: Matrix table with calculated RPKM value, raw gene counts for every gene and every sample

Submission date

Feb 28, 2022

Last update date

Mar 01, 2022

Contact name

Hiroki Tanemura

Organization name

Daiichi sankyo co., LTD.

Street address

2716-1 Kurakake, Akaiwa, Chiyoda-machi, Ohra-gun

City

Gunma