|
| Status |
Public on Aug 05, 2018 |
| Title |
ctrl_atac_1 |
| Sample type |
SRA |
| |
|
| Source name |
Male Chronic Myelogenous Leukemia (CML) cell line derived from KBM-7
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HAP1
genotype/variation: control
|
| Growth protocol |
HAP1 cells were cultivated in IMDM (ThermoFisher Scientific) supplemented with 10% Fetal Bovine Serum and 1% Penicillin/Streptamycin
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Illumina Nextera Library prep kit (FC-121-1030)
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
ctrl_atac_1
|
| Data processing |
Low quality reads and adaptors were removed using TrimGalore v0.3.3
Illumina spike-in PhiX were removed using BBMap v37.4
clean reads in fastq format were aligned to the human genome build hg19 using bwa mem v0.7.5a with default parameters
reads with mapq<20, improperly aligned reads and reads aligning to mitochondrial chromosome were filtered using SAMtools v0.1.19
peak calling was performed using MACS2 v2.1.0 with “--broad-cutoff 0.1 -f 'AUTO' -g hs -m 5 50 --bw 150 --fix-bimodal --extsize 100 -q 0.01” as parameters
resulting peaks were refined using the bdgcmp function of MACS2 v2.1.0 with the 'ppois' method
bedGraph files containing refined peaks were converted to bigWig format using the tool, bedGraphToBigWig v4 and visualized in the UCSC genome browser
Genome_build: hg19
Supplementary_files_format_and_content: tracks (peaks) in bigWig file format
|
| |
|
| Submission date |
Feb 23, 2018 |
| Last update date |
Aug 05, 2018 |
| Contact name |
Roza Berhanu Lemma |
| E-mail(s) |
[email protected]
|
| Phone |
+4740975997
|
| Organization name |
University of Oslo
|
| Department |
Department of Biosciences
|
| Lab |
Odd Stokke Gabrielsen
|
| Street address |
Blindernveien 31
|
| City |
Oslo |
| ZIP/Postal code |
0371 |
| Country |
Norway |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
|
| Relations |
| BioSample |
SAMN08584277 |
| SRA |
SRX3738173 |
