|
| Status |
Public on Dec 12, 2016 |
| Title |
K562 CD24-low sorted replicate 2 |
| Sample type |
SRA |
| |
|
| Source name |
K562
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: K562
cell type: low sorted
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Tagmentation was performed as previously described (Buenrostro et al., 2013)
Purified DNA was barcoded using a single unique adapter (i5)
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Library strategy: ATAC-seq
fastq files were aligned to the hg19 genome using Bowtie2 using the following specifications -S -X2000 -p10 -m1 --very-sensitive
Duplicates were removed and library size was estimated using PICARD tools
peaks were called using MACS2 with the --nomodel setting
Genome_build: hg19
Supplementary_files_format_and_content: bw files for UCSC upload were generated using bedtools
|
| |
|
| Submission date |
Dec 21, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Howard Chang |
| E-mail(s) |
howchang@stanford.edu
|
| Phone |
650-725-7022
|
| Organization name |
Stanford University
|
| Department |
Dermatology
|
| Street address |
269 Campus Drive
|
| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE76224 |
Single-cell epigenomic variability reveals functional cancer heterogeneity |
|
| Relations |
| BioSample |
SAMN04359741 |
| SRA |
SRX1495143 |
