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Sample GSM1573119 Query DataSets for GSM1573119
Status Public on Dec 24, 2015
Title WGC023779R
Sample type SRA
Source name Lung cells
Organism Homo sapiens
Characteristics cell type: Non-small-cell lung cancer (NSCLC) cells
cell line: A549
genotype: FOXD3 knockdown
group_tag: FOXD3
Treatment protocol A549 is a human non-small-cell lung cancer (NSCLC) cell line and it was used for constructing cell strain with FOXD3 knockdown. FoxD3 SMART pool(Cat. L-009152-00-0005) was purchased from Dharmacon/Thermo Fisher Scientific. Transfection of the siRNA oligonucleotide duplexes was performed in a 6-well plate (1 × 10 5cells per well) with Lipofectamine 2000 (Invitrogen, Inc.), using the methods recommended by the manufacturer. Using western blotting and real-time PCR, knockdown of FoxD3 with siRNA was examined 72 h after siRNA transfection.
Growth protocol A549 was cultured with MEM which was supplemented with 10% fetal bovine serum (FBS), 2 mmol/ l glutamine, 100 units/mL penicillin and 100 μg/mL streptomycin in a humidified atmosphere of 95% air and 5% CO2 at 37°C.
Extracted molecule total RNA
Extraction protocol RNA was extracted using Qiagen RNeasy MinElute Cleanup Kit
RNA libraries were prepared for sequencing using standard Illumina protocols (TruSeq RNA Sample Preparation Kit )
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
Data processing Illumina RTA1.18.61 software used for basecalling.
Sequenced reads were mapped to hg19 whole genome and transcriptome (Refseq) using TopHat v2.0.12 with parameters --bowtie1 --mate-inner-dist 0 --mate-std-dev 80 --prefilter-multihits --read-realign-edit-dist 0 --read-mismatches 2 --no-coverage-search --no-novel-juncs --no-novel-indels --microexon-search. The version of Bowtie was 1.1.0.
Fragments Per Kilobase of exon per Megabase of library size (FPKM) for Refseq genes were calculated using Cufflinks v2.0.2 with parameters --frag-bias-correct --multi-read-correct --compatible-hits-norm.
The gene expression differences were calculated using Cuffdiff with parameters --frag-bias-correct --multi-read-correct --compatible-hits-norm --library-norm-method geometric --dispersion-method pooled. And genes with false discovery rate (FDR) < 0.01 and fold change > 2 were defined as differentially expressed genes.
Genome_build: hg19
Supplementary_files_format_and_content: 6 files for corresponding samples include FPKM values of genes, 1 file lists all differentially expressed genes and 1 file lists differentially expressed genes after screening.
Submission date Dec 24, 2014
Last update date May 15, 2019
Contact name Jianru Xiao
Organization name Changzheng Hospital, Second Military Medical University
Department Department of Orthopedics Oncology
Street address 415 Fengyang Road
City Shanghai
ZIP/Postal code 200003
Country China
Platform ID GPL16791
Series (1)
GSE64513 FOXD3 is a novel tumor suppressor in lung cancer
BioSample SAMN03273182
SRA SRX824064

Supplementary file Size Download File type/resource
GSM1573119_WGC023779R_genes_expr_anno.txt.gz 1.8 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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