|
| Status |
Public on Jan 05, 2016 |
| Title |
A375-control |
| Sample type |
SRA |
| |
|
| Source name |
A375_malanoma_control
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: A375
cell type: Melanoma cell line
transfected with: pcDNA empty plasmid
genotype/variation: vector control
|
| Treatment protocol |
IGFBP5-A375 (Sample 1) was stabely transfected with pcDNA-IGFBP5, which result in over expression of IGFBP5. A375-control (Sample 2) was stably transfected with pcDNA empty plasmids as control.
|
| Growth protocol |
cells were cultured in an incubator at 37°C, 5% CO2
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from two samples by TRIzol, and poly(A) RNA was enriched by Dynabeads mRNA Purification Kit according to manufacturer's instruction.
The whole transcriptome libraries were prepared by ion total RNA-seq kit v2 according to its user guide.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Ion Torrent PGM |
| |
|
| Description |
Sample 2
|
| Data processing |
Tophat v2.0.13 used for first-step mapping
Bowtie2 v2.2.4 used for secon-step mapping with the unmapped reads produced by Tophat
Combine two-step mapping using samtools v1.1, then calculated the RPKM for each gene using Cufflinks v2.2.0
Computation and visualization were achieved using the heatmap plus package in R.
DAVID v6.7 for functional analysis of specific genes
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include normalized RPKM values for each Sample
|
| |
|
| Submission date |
Jan 06, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
yadong yang |
| E-mail(s) |
yangyd@big.ac.cn
|
| Organization name |
Beijing Institute of Genomics
|
| Street address |
No.1-104 Beichen West Road, Chaoyang
|
| City |
Beijing |
| ZIP/Postal code |
100101 |
| Country |
China |
| |
|
| Platform ID |
GPL17301 |
| Series (1) |
| GSE64693 |
Next generation sequencing of A375 melanoma cell line revealed a complex regulatory network when IGFBP5 overexpressed |
|
| Relations |
| BioSample |
SAMN03275723 |
| SRA |
SRX831181 |
