NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM4153422 Query DataSets for GSM4153422
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

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap