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| Status |
Public on Oct 13, 2016 |
| Title |
GM12878_FACS_sorted_S_2 |
| Sample type |
SRA |
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| Source name |
ATCC cell line GM12878
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| Organism |
Homo sapiens |
| Characteristics |
cell line: GM12878
cell type: FACS sorted S group
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| Treatment protocol |
cells were fixed and sorted based on DAPI staining and ATAC-see color intensity
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| Growth protocol |
ATCC cell lines (GM12878, HT1080) were purchesed from ATCC and maintained in standerd protocol according to the instruction, and sorted with FACS.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
50K cells were used for ATAC-seq lib in every group of FACS sorted cells
Sequencing libraries were constructed using a modified version of the Illumina Nextera DNA Sample prep kit and using custom-made Tn5 transposase ( where Atto-590 labled adaptor)
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
Library strategy: ATAC-seq
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 |
Apr 04, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Xingqi Chen |
| E-mail(s) |
xingqi@stanford.edu
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| Organization name |
Stanford University
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| Lab |
Howard Chang's lab
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| Street address |
269 Campus Drive
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| City |
Palo Alto |
| State/province |
CA |
| ZIP/Postal code |
94305-5168 |
| Country |
USA |
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| Platform ID |
GPL18573 |
| Series (1) |
| GSE79921 |
ATAC-Seq to investigate the spatial choreography of the accessible genome |
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| Relations |
| BioSample |
SAMN04613690 |
| SRA |
SRX1681320 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2108587_GM12878_FACS_sorted_S_2.pe.q10.sort.rmdup.bed.gz |
56.8 Mb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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