|
| Status |
Public on Jun 22, 2018 |
| Title |
H1048_1_input |
| Sample type |
SRA |
| |
|
| Source name |
Small cell lung cancer
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: NCI-H1048
cell type: Small cell lung cancer
treatment: exponentially growing cells with no infection
chip antibody: none
|
| Treatment protocol |
All parental cell lines were gowring exponentially upon harvest. Cells were lentivirally infected with sgRNA for knockout.
|
| Growth protocol |
NCI-H1048 cells were cultured in HITES, NCI-H128 cells were cultured in RPMI with 20% FBS and penicillin/streptomycin. All other cells were cultured in RPMI with 10% FBS and penicillin/streptomycin or HITES, .
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cell lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared using Illumina TruSeq ChIP Sample Prep kit following manufacture's protocol. Briefly, ChIP DNA was end-repaired, 3’-adenylated, and then ligated with indexed adaptor. These DNA was size selected (200-400 bp) via agarose gel electrophoresis, and PCR amplified. Final products were purified using AMPure XP beads.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Sequencing reads were mapped into reference human genome hg19 using Bowtie2
Peakcalling was done using MACS2 FDR cut off 5% with broad peak and narrow peak option for H3K27ac and POU2F3, respectively
The H3K27ac peaks in knockout experiment were merged with corresponding control ChIP-seq using BEDtools
Normalized tag count was calculated using MACS2.0
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files contain normalized tag count
|
| |
|
| Submission date |
May 30, 2018 |
| Last update date |
Jun 22, 2018 |
| Contact name |
Olaf Klingbeil |
| E-mail(s) |
[email protected]
|
| Organization name |
Cold Spring Harbor Laboratory
|
| Street address |
1 Bungtown Road
|
| City |
Cold Spring Harbor |
| State/province |
New York |
| ZIP/Postal code |
11724 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE115123 |
POU2F3 is a master regulator of a tuft cell-like variant of small cell lung cancer [ChIP-seq] |
| GSE115124 |
POU2F3 is a master regulator of a tuft cell-like variant of small cell lung cancer |
|
| Relations |
| BioSample |
SAMN09284066 |
| SRA |
SRX4142984 |
