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| Scope: Self Platform Samples Series Family Format: HTML SOFT MINiML Amount: Brief Quick GEO accession: |  |
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| Sample GSM1972148 | Query DataSets for GSM1972148 |
| | Status | Public on Oct 05, 2016 | | Title | HT1080_fixed_rep2 | | Sample type | SRA | | Source name | ATCC Cell line HT1080 | | Organism | Homo sapiens | | Characteristics | cell line: ATCC Cell line HT1080genotype/variation: with fixation #2 | | Treatment protocol | human neutrophils were purfied from healthy volunteer according to the Stanford IRB protocol and maintained in RPMI-HEPES (10 mM) during 30nM PMA (Phorbol myristate acetate ) and PAD4 inhibitor (200 μM Cl-amidine ) treatment. | | Growth protocol | ATCC cell lines (GM12878, HT1080) were purchesed from ATCC and maintained in standerd protocol according to the instruction, human neutrophils were purfied from healthy volunteer according to the Stanford IRB protocol and maintained in RPMI-HEPES (10 mM) during 30nM PMA (Phorbol myristate acetate ) and PAD4 inhibitor (200 μM Cl-amidine ) treatment. | | Extracted molecule | genomic DNA | | Extraction protocol | 50K cells were used for ATAC-seq lib in both fixed (1% formaldehyde 10mins at RT ) and unfixed samples. After imaging, ~50K cells were used for ATAC-seq library constructionSequencing 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) | | Library strategy | OTHER | | Library source | genomic | | Library selection | other | | Instrument model | Illumina NextSeq 500 | | Description | ATCC Cell line HT1080 with fixation #2 | | Data processing | library strategy: ATAC-seqReads 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 fromm 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 RGenome_build: hg19Supplementary_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 14, 2015 | | Last update date | May 15, 2019 | | Contact name | Xingqi Chen | | E-mail(s) | [email protected] | | Organization name | Stanford University | | Lab | Howard Chang's lab | | Street address | 269 Campus Drive | | City | Palo Alto | | State/province | CA | | ZIP/Postal code | 94305-5168 | | Country | USA | | Platform ID | GPL18573 | | Series (1) | | GSE76006 | ATAC-Se1 to investigate the spatial choreography of the accessible genome |
| | Relations | | BioSample | SAMN04337129 | | SRA | SRX1482102 |
| Supplementary file | Size | Download | File type/resource | | GSM1972148_HT1080_fixed_rep2.bed.gz | 209.0 Mb | (ftp)(http) | BED | SRA Run Selector | | Raw data are available in SRA | | Processed data provided as supplementary file |
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