 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Oct 07, 2020 |
| Title |
ATAC-seq KD_HBVneg_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
KD_HBVneg_rep1
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HepG2
gender: male
age: 15 yr
passage: 20-23
tissue: Liver
genotype/variation: KD
|
| Growth protocol |
Cells were cultured for 10 days. Media was changed every 3 days and passaged if cells were confluent.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells (5 x 104) were washed in cold PBS and lysed in 50 µl of lysis buffer (10 mM Tris HCl pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630). Following lysis and centrifugation, nuclei were used for transposition using Illumina Tagment DNA TDE1 Enzyme and Buffer Kit (Cat# 20034197) per manufacturer’s protocol. The transposed DNA was cleaned using Qiagen Reaction Cleanup kit (Cat# 28204), eluted in 10 µL elution buffer and stored at -20oC.
Transposed DNA was PCR amplified using primers containing unique adapters. Amplified library was purified using Qiagen MinElute PCR Purification Kit (Cat#28004). Pairedend 2x50 bp sequencing was performed using a HiSeq2500 system (Illumina).
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
HepAD38 -HBV DDX5KD
|
| Data processing |
Data quality control was performed using FastQC v0.11.8. Raw sequencing reads were mapped to hg19 using bowtie2.3.4.3 [2] with “-X 2000”.
All other parameters were kept as default. Duplicate and low quality (MAPQ<30) reads are removed using PicardTools2.21.6
Differential chromatin accessible regions/peaks between DDX5 WT and KD were obtained using MACS2.1.2, peaks overlapped with the hg19 blacklist(wgEncodeDacMapabilityConsensusExcludable.bed) are removed
HOMER4.9.1 was used to annotate the peaks with their adjacent genes that were then subjected to pathway analysis against all biological processes from gene ontology (GO) using Matescape
The IGV tracks were made using bamCoverage from DeepTools3.3.0 with parameter “-p 3 -bs 5 --normalizeUsing CPM -- ignoreDuplicates” and visualized by IGV browser
Genome_build: hg19
Supplementary_files_format_and_content: IGV tracks: bigwig files
Supplementary_files_format_and_content: peak files: .bed files
|
| |
|
| Submission date |
Oct 05, 2020 |
| Last update date |
Oct 07, 2020 |
| Contact name |
Majid Kazemian |
| E-mail(s) |
[email protected]
|
| Organization name |
Purdue university
|
| Street address |
201 S. University Street
|
| City |
West Lafayette |
| State/province |
Indiana |
| ZIP/Postal code |
47907 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE131257 |
RNA Helicase DDX5, a Negative Regulator of Wnt Activation and Hepatocyte Reprogramming in Hepatitis B Virus-associated Hepatocellular Carcinoma |
|
| Relations |
| BioSample |
SAMN16376842 |
| SRA |
SRX9246485 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4818345_KD_HBVneg_rep1.bw |
295.4 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
| Raw data are available in SRA |
|
|
|
|
 |
