|
| Status |
Public on Jan 04, 2016 |
| Title |
A375-pRNAT-scramble |
| Sample type |
SRA |
| |
|
| Source name |
A375_scamble
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Melanoma cell line
cell line: A375
|
| Treatment protocol |
Sample 1 was stabely transfected with pcDNA3 vector, which resulted in as a negative control for OE. Sample 2 was stabely transfected with pcDNA3-MAGE-A1 plasmids as overexpression of MAGE-A1.Sample 3 was stabely transfected with pRNAT-scramble vector, which resulted in as a negative control for KD.Sample 4 was stabely transfected with pRNAT-shMAGE-A1 plasmids as knockdown of MAGE-A1.
|
| 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 |
| |
|
| 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 RPKM values for each Sample
|
| |
|
| Submission date |
Mar 13, 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) |
| GSE66859 |
MAGE-A1 Promotes Proliferation, Migration and Invasion of Human Melanoma Cells through RNA-SEQ Analysis via Affecting C-JUN-IL8-ARHGAP29 Network |
|
| Relations |
| BioSample |
SAMN03406685 |
| SRA |
SRX955770 |
