GEO Accession viewer

NCBI > GEO > Accession Display

Not logged in | Login

GEO help: Mouse over screen elements for information.

Sample GSM4909877

Query DataSets for GSM4909877

Status

Public on Oct 01, 2021

Title

SGC7901_ILF3_siRNA#1

Sample type

SRA

Source name

gastric cancer cell

Organism

Homo sapiens

Characteristics

cell type: SGC7901
transfection: ILF3 siRNA#1

Treatment protocol

SGC7901 cells were seeded into 6-well plates and grown overnight. The next day, when the cell plating density reached 20%-30%, GC cells were transfected with NC siRNAs and the ILF2/ILF3-targeted siRNAs (final concentration, 50 nM) by Lipofectamine 2000 (Invitrogen) according to the manufacturer’s instructions. At 48 h post-transfection, cells were harvested for RNA sequencing.

Growth protocol

The human gastric cancer cell line SGC7901 was purchased from the Shanghai Cell Bank of Chinese Academy of Sciences (Shanghai, China). The gastric cancer cell line SGC7901 was cultured in DMEM medium containing 10% fetal bovine serum (FBS), 100 U/mL penicillin, 100 U/mL streptomycin and 0.03% glutamine at 37 oC in 5% CO2.

Extracted molecule

total RNA

Extraction protocol

Gastric cancer cells were grown in 6-well plates and transfected with NC siRNAs and the ILF2/ILF3-targeted siRNAs. After 48 hours, remove the medium and directly add 800μL Trizol into the 6-well plate to harvest samples. Total RNA was extracted using Trizol reagent (Invitrogen, USA) according to the manufacturer’s instructions. The RNA purity and concentration was checked using the NanoPhotometer spectrophotometer (IMPLEN, CA, USA).
A total amount of 1.5 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer's recommendations and index codes were added to attribute sequences to each sample. MRNA was purified from total RNA using poly-T oligo-attached magnetic beads.

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 4000

Data processing

Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reads were mapped to human genome assembly GRCh38 (ftp://ftp.ensembl.org/pub/release-89/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.toplevel.fa.gz) using HISAT2 with default parameters.
HTSeq v0.11.2 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. GTF file:ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_26/gencode.v26.annotation.gtf.gz.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text file include count and FPKM values for each Sample

Submission date

Nov 16, 2020

Last update date

Oct 01, 2021

Contact name

Qin Shanshan

E-mail(s)

[email protected]

Organization name

Institute of Basic Medical Sciences, School of Basic Medical Sciences, Hubei University of Medicine

Street address

Renmin Road 30, Maojian District