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| Status |
Public on Dec 20, 2016 |
| Title |
CD24plusplus1 |
| Sample type |
SRA |
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| Source name |
K562
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| Organism |
Homo sapiens |
| Characteristics |
cell type: CML cell line
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| 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)
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
CD24plus-CD24plus
Started from a CD24 positive K562 cell population. Re-sorted after 5 days for CD24. CD24 positive at day5. Replicate1
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| Data processing |
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
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| Submission date |
Dec 19, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Howard Chang |
| E-mail(s) |
howchang@stanford.edu
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| Phone |
650-725-7022
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| Organization name |
Stanford University
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| Department |
Dermatology
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| Street address |
269 Campus Drive
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| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
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| Platform ID |
GPL18573 |
| Series (1) |
| GSE76224 |
Single-cell epigenomic variability reveals functional cancer heterogeneity |
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| Relations |
| BioSample |
SAMN06166444 |
| SRA |
SRX2436347 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2433343_CD24plus-CD24plus_1_peaks.narrowPeak.gz |
44.9 Kb |
(ftp)(http) |
NARROWPEAK |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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