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Sample GSM2011184 Query DataSets for GSM2011184
Status Public on Sep 26, 2016
Title 2b_CNRTL_ASO_DOXORUBICIN_REP4
Sample type SRA
 
Source name FL3_CNRTL_ASO_DOXORUBICIN
Organism Homo sapiens
Characteristics cell line: FL3
cell type: Early passage human diploid fibroblasts
transfected with: control antisenses oligonucleotides (ASOs)
treated with: 0.2ug/mL doxorubicin
Treatment protocol 300,000 fibroblasts with transfected with 100nM ASO using lipofectamine. 24 hours later, cells were treated with 0.2ug/mL doxorubicin or vehicle alone for a total of 12 hours.
Growth protocol Early passeage FL3 human diploid fibroblasts were obtained from ATCC and grown in standard DMEM + 10% serum.
Extracted molecule genomic DNA
Extraction protocol 50,000 cells were used for each transposition reaction. Nuclei were prepared prior to transposition.
Sequencing libraries were constructed using a modified version of the Illumina Nextera DNA Sample prep kit.
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina HiSeq 2000
 
Data processing Reads were trimmed for adaptor sequence, then mapped to UCSC hg19 using bowtie, duplicate fragments were then removed using Picard. Peaks were called using the ZINBA algorithm, which was first applied to each dataset independently, using the following parameters: a 300bp window, 50bp offset, background and enriched components were modeled using the intercept, while the zero-inflated component was modeled using alignability, a posterior probability of 0.99 was used to select the set of significant regions. The peak sets from the same cell-type and number of cells were merged.
Number of Raw reads in each peak was calculated using in house generated script, and data matrix was normalized using R
Genome_build: hg19
Supplementary_files_format_and_content: Peak files are in tab seperated format, which includes the following columns: chromosome, start, stop, name, arbitrary score (1000), strand
 
Submission date Dec 30, 2015
Last update date May 15, 2019
Contact name Adam Schmitt
E-mail(s) amschmit@stanford.edu
Phone 650-736-0305
Fax 650-723-8762
Organization name Stanford University
Department Department of Dermatology
Lab Howard Y. Chang
Street address 269 Campus Drive
City Stanford
State/province CA
ZIP/Postal code 94305-5168
Country USA
 
Platform ID GPL11154
Series (2)
GSE76417 ATAC-Seq on DNA damaged human fibroblasts
GSE76420 LncRNA DINO guides DNA damage signaling
Relations
BioSample SAMN04377134
SRA SRX1508403

Supplementary file Size Download File type/resource
GSM2011184_2b_CNRTL_ASO_DOXORUBICIN_REP4.peakprob0.99.peaks.bed.gz 1.2 Mb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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