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Sample GSM8342000

Query DataSets for GSM8342000

Status

Public on Aug 30, 2024

Title

Hct116NCBP2_2

Sample type

SRA

Source name

colorectal cancer

Organism

Homo sapiens

Characteristics

tissue: colorectal cancer
cell line: Hct116
cell type: Hct116 colorectal cancer cells
treatment: overexpressed NCBP2

Extracted molecule

total RNA

Extraction protocol

Culture medium were removed, washed by PBS, and RNA was harvested using Trizol reagent. Illumina NovaSeq X Plus 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 X Plus

Data processing

Integrative Genomcs Viewer software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Fragment Per Kilobase of exon model per Million mapped reads(FPKM) were calculated using a standard protocol from MajorBio company. 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 of MajorBio.
Assembly: mm9
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample .

Submission date

Jun 20, 2024

Last update date

Aug 30, 2024

Contact name

shoudong ye

Organization name

Anhui University

Department

Cell Biology

Street address

No 111, Jiu Long Road