|
| Status |
Public on Sep 17, 2019 |
| Title |
H3K27ac ChIP for EBC-1 |
| Sample type |
SRA |
| |
|
| Source name |
EBC1_H3K27ac
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: EBC-1
cell type: lung squamous cell carcinoma (LUSC) cell lines
chip antibody: acetyl-histone H3K27 (Abcam, ab4729)
|
| Treatment protocol |
N/A
|
| Growth protocol |
Cells were maintained in RPMI-1640 with 10% fetal bovine serum and 1% penicillin–streptomycin.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
For H3K27ac, Sox2 and p63 ChIP, cells were cross-linked with 1% formaldehyde and lysed. Chromatin in the lysates was sonicated and histone-DNA complexes were isolated with antibodies. For Brn2 ChIP, cells were cross-linked with disuccinimidyl glutarate and formaldehyde. Nuclei were extracted, digested with micrococcal nuclease and sonicated. Then, histone-DNA complexes were isolated with ant-Brn2 antibody.
Up to 10 ng of DNA was used for the library construction using NEBNext Ultra II DNA Library Prep Kit. The finished double strand DNA libraries were quantified by Agilent Bioanalyzer according to manufacturer’s protocol. Uniquely indexed libraries were pooled in equimolar ratios and sequenced on an Illumina NextSeq 500 with paired-end 75bp reads.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
ts_hw_ebc1_ab4729_chip_0414_13c_S10_ALL
|
| Data processing |
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie2 with -k 1 option
Peaks were identified by MACS
Genome_build: hg19/GRCh37
Supplementary_files_format_and_content: BED
|
| |
|
| Submission date |
Sep 16, 2019 |
| Last update date |
Sep 17, 2019 |
| Contact name |
Hideo Watanabe |
| E-mail(s) |
hideo.watanabe@mssm.edu
|
| Organization name |
Icahn School of Medicine at Mount Sinai
|
| Department |
Department of Medicine, Division of Pulmonary, Critical Care and Sleep Medicine
|
| Lab |
Hideo Watanabe
|
| Street address |
One Gustave L. Levy Place
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10029 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE137459 |
Identification of a unique subtype of lung squamous cell carcinoma defined by SOX2 and a neural differentiation factor BRN2 [ChIP-seq] |
| GSE137461 |
Identification of a unique subtype of lung squamous cell carcinoma defined by SOX2 and a neural differentiation factor BRN2 |
|
| Relations |
| BioSample |
SAMN12757114 |
| SRA |
SRX6852793 |
