|
| 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 |
|
| Relations |
| BioSample |
SAMN03273182 |
| SRA |
SRX824064 |
