|
| Status |
Public on Jul 07, 2016 |
| Title |
A375_shNT_day4_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
A375_shNT_day4
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: A375
cell type: melanoma cell line
transfected with: lenti-viral based shNT
time point: 4 days after transfection
|
| Treatment protocol |
Cells were infected with lenti-viral based shNT or shIno80, cells were harvested 2, 3, and 4 days after infection
|
| Growth protocol |
A375 cells were maintained in 10% FBS DMEM
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were harvested and total RNA was extracted by Thermo RNA kit
The sequencing library was generated by Truseq RNA sample preparation kit according to the instruction
Truseq RNA sample preparation kit V2
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Gene expression 4 days after transfection
|
| Data processing |
Aligned with TopHat2 version 2.0.4 with the following parameters: -g 10
FPKM measurements obtained using CuffLinks version 2.0.2
Genome_build: hg19
Supplementary_files_format_and_content: FPKM: 1st column = RefSeq ID, 2nd column = fragments per kilobase of exon per million mapped reads (FPKM value)
|
| |
|
| Submission date |
Jun 07, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Li Wang |
| Organization name |
NIH
|
| Street address |
111 T.W. Alexander Dr
|
| City |
Durham |
| ZIP/Postal code |
27709 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE82333 |
INO80 governs super-enhancer-mediated oncogenic transcription and tumor growth in melanoma [RNA-seq] |
| GSE82334 |
INO80 governs super-enhancer-mediated oncogenic transcription and tumor growth in melanoma |
|
| Relations |
| BioSample |
SAMN05214346 |
| SRA |
SRX1829897 |
