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| Status |
Public on Sep 26, 2016 |
| Title |
14b_DINO_ASO2_DOXORUBICIN_REP4 |
| Sample type |
SRA |
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| Source name |
FL3_DINO_ASO2_DOXORUBICIN
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| Organism |
Homo sapiens |
| Characteristics |
cell line: FL3
cell type: Early passage human diploid fibroblasts
transfected with: antisenses oligonucleotides (ASOs) targeting lncRNA DINO
treated with: 0.2ug/mL doxorubicin
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| 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.
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| Growth protocol |
Early passeage FL3 human diploid fibroblasts were obtained from ATCC and grown in standard DMEM + 10% serum.
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| 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.
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
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| 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
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| Submission date |
Dec 30, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Adam Schmitt |
| E-mail(s) |
amschmit@stanford.edu
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| Phone |
650-736-0305
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| Fax |
650-723-8762
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| Organization name |
Stanford University
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| Department |
Department of Dermatology
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| Lab |
Howard Y. Chang
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| Street address |
269 Campus Drive
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| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305-5168 |
| Country |
USA |
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| Platform ID |
GPL11154 |
| Series (2) |
| GSE76417 |
ATAC-Seq on DNA damaged human fibroblasts |
| GSE76420 |
LncRNA DINO guides DNA damage signaling |
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| Relations |
| BioSample |
SAMN04377150 |
| SRA |
SRX1508419 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2011200_14b_DINO_ASO2_DOXORUBICIN_REP4.peakprob0.99.peaks.bed.gz |
2.2 Mb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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