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Sample GSM1693908 Query DataSets for GSM1693908
Status Public on Sep 01, 2016
Title ChIP_NPAT_U2OS
Sample type SRA
 
Source name U2OS
Organism Homo sapiens
Characteristics cell line: U2OS
cell type: osteosarcoma
chip antibody: NPAT (sc-67007, Santa Cruz Biotechnology)
Growth protocol cells were cultured in media supplemented with penicillin/streptomycin and 10% FBS under standard culture conditions.
Extracted molecule genomic DNA
Extraction protocol Cells were cross-linked by 1% formaldehyde, and DNA was sonicated to 200- 400 bp fragments. Antibodies (5 µg) were added and collected using protein G Sepharose (GE). Cross-links were reversed and proteins digested by incubation with proteinase K at 65 °C overnight. DNA was then purified using Qiagen PCR purification kit.
Libraries were constructed according to Illuminas standard protocol.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer IIx
 
Data processing Sequencing reads were mapped to the human genome (NCBI36)
peaks called with koli as described before
Genome_build: hg18
Supplementary_files_format_and_content: Chromosome, peak start and peak end refers to to genome assembly NCBI36; Peak summit defined as the point of maximum height that is closest to the center of the peak; Peak height the maximum number of overlapping sequences; Fold change calculated from the areas of the peaks in the ChIP sample vs. IgG sample; p-value probability of observing the difference between the sequence counts in the ChIP sample and IgG control by chance estimated using Winflat program
 
Submission date May 21, 2015
Last update date May 15, 2019
Contact name Maria Sokolova
E-mail(s) maria.fulop@helsinki.fi
Organization name University of Helsinki
Department Institute of Biotechnology
Lab Nuclear Actin Lab
Street address Viikinkaari 5
City Helsinki
ZIP/Postal code 00014
Country Finland
 
Platform ID GPL10999
Series (2)
GSE69147 Histone genes transcription regulators binding in human cancer (U2OS) and normal (hTERT-RPE1) cells
GSE69149 Histone gene regulation in normal and tumor cells
Relations
BioSample SAMN03704244
SRA SRX1036441

Supplementary file Size Download File type/resource
GSM1693908_NPAT-U2OS.txt.gz 6.1 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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