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Sample GSM1462554 Query DataSets for GSM1462554
Status Public on Aug 24, 2015
Title Input DNA
Sample type SRA
Source name primary dermal fibroblasts
Organism Homo sapiens
Characteristics body site: abdomen skin
passage: 4-6
antibodies: none
Extracted molecule genomic DNA
Extraction protocol Chromatin from 10 milions fixed cells was fragmented to a size range of 100–300 bases with a Diagenode Bioruptor. Solubilized chromatin was immunoprecipitated with two different antibody against CSL. Antibody–chromatin complexes were pulled-down using protein A-sepharose, washed and then eluted. After cross-link reversal and proteinase K treatment, immunoprecipitated DNA was extracted with phenol-chloroform, ethanol precipitated, and treated with RNase.
ChIPed DNA was quantified by fluorometry on the Qubit system (Invitrogen). A total of 10 ng DNA were used for library preparation using NEBNext® ChIP-Seq Library Prep Reagent Set for Illumina, as recommended by the manufacturer.
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2000
Data processing ChIP-seq reads were aligned to the hg19 genome assembly using Burrows-Wheeler Aligner with default parameters
peaks were called using MACS software version 1.4 with default parameter
Genome_build: hg19
Supplementary_files_format_and_content: bed files were generated by MACS as output of the analysis
Submission date Jul 30, 2014
Last update date May 15, 2019
Contact name Paola Ostano
Organization name Fondazione Edo ed Elvo Tempia
Street address via Malta 3
City Biella
ZIP/Postal code 13900
Country Italy
Platform ID GPL11154
Series (2)
GSE59942 Physical and functional CSL-p53 interactions underlie control of cancer stromal cell evolution [ChIP-seq]
GSE65474 Physical and functional CSL-p53 interactions underlie control of cancer stromal cell evolution
BioSample SAMN02947374
SRA SRX666594

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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