|
| Status |
Public on Jul 07, 2016 |
| Title |
A375_shNT_ATAC |
| Sample type |
SRA |
| |
|
| Source name |
human A375
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: A375
cell type: melanoma cell line
infected with: lenti-viral based shNT
time point: 2 days after infection
|
| Treatment protocol |
Cells were infected with lenti-viral based shNT or shIno80, cells were harvested 2 days after infection
|
| Growth protocol |
A375 cells were maintained in 10% FBS DMEM
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were harvested and counted, and lysed by ATAC-Seq lysis buffer
The sequencing library was generated by nextear DNA preparation kit according to the instruction
Nextera DNA sample preparation kit
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
library strategy: ATAC-seq
Aligned with Bowtie version 0.12.8 with the following parameters: -v 2 -m 1 --best --strata
Nucleosome signal was generated from the signal of fragments with insert length between 180 and 247 minus the signal of fragments with insert length less than 100
Genome_build: hg19
Supplementary_files_format_and_content: BedGraph: nucleosome signal normalized to reads per 10 million aligned reads
|
| |
|
| 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) |
| GSE82330 |
INO80 governs super-enhancer-mediated oncogenic transcription and tumor growth in melanoma [ATAC-seq] |
| GSE82334 |
INO80 governs super-enhancer-mediated oncogenic transcription and tumor growth in melanoma |
|
| Relations |
| BioSample |
SAMN05214318 |
| SRA |
SRX1829862 |
