|
| Status |
Public on Feb 05, 2019 |
| Title |
omniATAC-seq H838 |
| Sample type |
SRA |
| |
|
| Source name |
H838 lung cancer cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: H838
tissue: lung cancer cell line
|
| Growth protocol |
H1299, H727 and H838 cells were grown in 10cm culture-treated plates in RPMI1640 + 10% FBS + 1x P/S media. Cells were collected by trypsinization with 0.05% Trypsin-EDTA.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
RNA was collected using Trizol following manufacture's recommendation. mRNA for nanoCAGE was extracted using Dynabeads mRNA DIRECT kit following manufacture's recommendation. DNA was extracted with Quick-DNA Miniprep Kit.
CAGE-seq was generated using CAGE Preparation Kit from DNAFORM. nanoCAGE-seq was generated following protocol designated in Poulain et al. 2017. WGBS-seq was generated using EZ DNA Methylation-Direct kit. RNA-seq was generated using TruSeq RNA Library Prep Kit v2. Published omniATAC-seq was followed to generate ATAC-seq data.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
All libraries were sequenced on Illumina NextSeq 500 platforms. Reads were adapter-trimmed with cutadapt. For nanoCAGE library, we also trimmed the first 17 bases from read 1 to remove adapter and index sequences.
RNA reads were aligned to hg19 genome using STAR. nanoCAGE reads were aligned to hg38.
WGBS reads were aligned to hg19 using bismark with standard parameters.
CAGE reads were trimmed to 100bp and aligned to hg19 using HISAT.
omniATAC reads were aligned to hg19 using bwa-mem.
Genome_build: hg19, hg38
Supplementary_files_format_and_content: RNA and omniATAC bam files were converted to bigWig format. nanoCAGE-seq and CAGE-seq CTSS bedgraphs were generated with CAGEr package. WGBS methylation values of CpGs from bismark analysis is available.
|
| |
|
| Submission date |
May 02, 2018 |
| Last update date |
Feb 06, 2019 |
| Contact name |
Daofeng Li |
| E-mail(s) |
lidaof@gmail.com
|
| Phone |
(314) 286-0866
|
| Organization name |
Washington University in St. Louis
|
| Department |
Genetics
|
| Lab |
Ting Wang Lab
|
| Street address |
4515 McKinley Avenue
|
| City |
SAINT LOUIS |
| State/province |
MO |
| ZIP/Postal code |
63110 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE113946 |
Widespread transposable element-driven oncogene expression in cancers |
|
| Relations |
| BioSample |
SAMN09010768 |
| SRA |
SRX4020920 |
