|
| Status |
Public on May 07, 2015 |
| Title |
Control Experiments Set 2 |
| Sample type |
SRA |
| |
|
| Source name |
Mixture of GM12878 and HL-60
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: Mixture of GM12878 and HL-60
molecule subtype: Accessible genomic DNA
|
| Biomaterial provider |
Coriell Cell repositories (GM12878)
http://ccr.coriell.org/Sections/Search/Search.aspx?PgId=165&q=GM12878
|
| Growth protocol |
Cells grown under standard conditions. Patski and HEK293T were cultured in DMEM supplemented with 10% FBS. GM12878 and HL-60 were grown in RPMI 1640 supplemented with 15% FBS.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Intact nuclei were isolated with ATAC-seq cold lysis buffer suplemented with protease inhibitors.
Genomic DNA in intact nuclei was simultaneously molecularly tagged and fragmented. Nuclei tagged with 1 of 96 barcodes were pooled and then redistributed into wells of a PCR plate (15-25 nuclei per well) using a cell sorter. A second barcode was introduced during library amplification.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina MiSeq |
| |
|
| Description |
Controls Set 2
|
| Data processing |
library strategy: ATAC-seq
qseq files generated with OLB v1.9.3
barcodes updated and fastq files generated with custom perl script
Adapters trimmed with Trimmomatic v0.32
Reads mapped with BWA v0.7.8-r749-dirty
Unmapped reads and mitochondrial reads filtered out.
Duplicate fragments removed with picard v1.105
Reads overlapping known hypersensitive sites were counted for each barcode to generate DHS matrix with custom python script
Genome_build: hg19 or mm9
Supplementary_files_format_and_content: tab-separated vector - first 4 columns contain location information for each hypersensitivity site, remaining columns include counts of reads overlapping that site assigned to each barcode. Please see 'readme.txt' for detailed description..
|
| |
|
| Submission date |
Mar 31, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Darren A. Cusanovich |
| E-mail(s) |
darrenc@arizona.edu
|
| Organization name |
University of Arizona
|
| Department |
Cellular and Molecular Medicine
|
| Street address |
1230 N Cherry Avenue, BSRL 421
|
| City |
Tucson |
| State/province |
AZ |
| ZIP/Postal code |
85721 |
| Country |
USA |
| |
|
| Platform ID |
GPL15520 |
| Series (2) |
| GSE67446 |
Multiplex Single Cell Profiling of Chromatin Accessibility by Combinatorial Cellular Indexing [ATAC-seq] |
| GSE68103 |
Multiplex Single Cell Profiling of Chromatin Accessibility by Combinatorial Cellular Indexing |
|
| Relations |
| BioSample |
SAMN03452735 |
| SRA |
SRX974240 |
