|
| Status |
Public on Aug 03, 2016 |
| Title |
A549_shIno80_H3K56ac |
| Sample type |
SRA |
| |
|
| Source name |
human A549_shIno80
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: A549
cell type: lung cancer cell line
antibody vendor: Active motif
antibody cat. #: 39281
antibody lot #: 14013003
|
| Treatment protocol |
A549 infected with shNT or shIno80, was used for ChIP-Seq for corresponding factors 2 days after infection.
|
| Growth protocol |
A549 cell lines were obtained from ATCC, and cultured in DMEM supplemented with 10% fetal bovine serum (FBS).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Ino80 ChIP were performed as described previously. Briefly, A549 cells were fixed using 1% formaldehyde for 10 min, and 0.125 M glycine was added to stop the fixation. Cells were harvested, and DNA was fragmented to 300–500 bp by sonication with a micro-tip attached to a Misonix 3000 sonicator. Immunoprecipitation was performed with antibodies conjugated to Dynabeads protein G beads (Life Technology). ChIP DNA was eluted, reverse cross-linked, extracted by phenol/chloroform, and precipitated.
For ChIP-seq, 1 ng ChIP DNA or input DNA was used to generate sequencing libraries using the Nextera XT DNA sample preparation Kit (Illumina). Nextera XT DNA sample preparation kit (illumina)
|
| |
|
| 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 |
Aug 02, 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) |
| GSE85117 |
INO80 is required for oncogenic transcription and tumor growth in non-small cell lung cancer [ChIP-seq] |
| GSE85119 |
INO80 is required for oncogenic transcription and tumor growth in non-small cell lung cancer |
|
| Relations |
| BioSample |
SAMN05505545 |
| SRA |
SRX1995835 |
