|
| Status |
Public on Jul 07, 2016 |
| Title |
A375_shNT_Input |
| Sample type |
SRA |
| |
|
| Source name |
human A375
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: human A375
cell type: melanoma cell line
infected with: lenti-viral based shNT
time point: 48 hours after infection
|
| Treatment protocol |
80% confluent cells were used for ChIP-Seq analysis, or 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 fixed, harvested, and lysed, then submitted to sonication. The sonicated DNA was incubated with specific beads-conjugated antibody overnight. Then the beads were washed, and DNA was eluted, and quantified.
The sequencing library was generated by use of Nextera XT DNA preparation Kit
Nextera XT DNA preparation Kit
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
ChIP-Seq was performed 48 hours after infection
|
| Data processing |
Aligned with Bowtie version 0.12.8 with the following parameters: -v 2 -m 1 --best --strata
Genome_build: hg19
Supplementary_files_format_and_content: BedGraph: coverage 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) |
| GSE82332 |
INO80 governs super-enhancer-mediated oncogenic transcription and tumor growth in melanoma [ChIP-seq_NextSeq] |
| GSE82334 |
INO80 governs super-enhancer-mediated oncogenic transcription and tumor growth in melanoma |
|
| Relations |
| BioSample |
SAMN05214328 |
| SRA |
SRX1829876 |
