|
Status |
Public on Nov 08, 2019 |
Title |
Dox_rep2 ChIP-seq |
Sample type |
SRA |
|
|
Source name |
Mamary gland epithelial cell
|
Organism |
Homo sapiens |
Characteristics |
cell type: Breast adenocarcinoma gender: Female chip antibody: HA tag (abcam: ab9110) cell line: MCF-7 agent: doxycycline
|
Treatment protocol |
Cells were treated with doxycycline (50ng/ml) to induce PAX2 oeverexpresson, followed by tamoxifen (1uM) treatment for 6 hours.
|
Growth protocol |
MCF-7 cells were cultured in DMEM with 5% FBS
|
Extracted molecule |
genomic DNA |
Extraction protocol |
MCF-7 chromatin was sonicated and PAX2 bond genomic regions were isolated by using HA tag antibody. Libraries were prepared by Norwegian sequencing centre and CRUK genomics core facility
|
|
|
Library strategy |
ChIP-Seq |
Library source |
genomic |
Library selection |
ChIP |
Instrument model |
Illumina NextSeq 500 |
|
|
Description |
PAX2_ChIP_Dox_peaks.narrowPeak
|
Data processing |
Basecalling with Illumina 1.9 software FastX Toolkit (0.013) was used to filter out low quality reads, (min. 97% of bases should have quality score of 10). Command: fastq_quality_filter -v -q 10 -p 97 -i input file -o output file Quality filtered data was aligned to hg19 assembly with Bowtie 1.1.2. v=2, m=3, k=1. samtools (1.3.1) was used to convert sam files to bam files, and to remove duplicate in bam files peaks were called with macs2 (2.1.1) Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files include genomic coordinates of PAX2 (HA) peaks called in different treatments
|
|
|
Submission date |
Nov 07, 2019 |
Last update date |
Nov 10, 2019 |
Contact name |
Shixiong Wang |
E-mail(s) |
[email protected]
|
Phone |
+47-22845865
|
Organization name |
University of Oslo
|
Department |
Centre for Molecular Medicine Norway
|
Street address |
Gaustadalléen 21
|
City |
Oslo |
ZIP/Postal code |
0349 |
Country |
Norway |
|
|
Platform ID |
GPL18573 |
Series (1) |
GSE140060 |
Genome wide analysis of PAX2 chromatin interaction in MCF-7 cell |
|
Relations |
BioSample |
SAMN13229227 |
SRA |
SRX7114559 |