|
| Status |
Public on Sep 25, 2021 |
| Title |
K562 ++ untreated ATAC-seq [WT_ut_1_S1] |
| Sample type |
SRA |
| |
|
| Source name |
K562 ++ untreated
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: K562
sledai: ++ untreated
replicate: replicate 1
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
MiniElute kit
ATAC libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Created Bowtie index using the GrCh37 assembly of the human genome
Estimated peaks with MACS2 using parameters -q 0.05 --nolambda --slocal 1000 --llocal 10000 -m 5 50 --shift 0 --extsize 200 --fe-cutoff 1.0.
Differential expression analysis performed using DESeq2
Genome_build: GrCh37
Supplementary_files_format_and_content: Differential expression analysis
|
| |
|
| Submission date |
Jul 28, 2020 |
| Last update date |
Sep 25, 2021 |
| Contact name |
Carol Webb |
| E-mail(s) |
carol-webb@ouhsc.edu
|
| Organization name |
OUHSC
|
| Department |
Department of Medicine
|
| Street address |
Stephenson Parkway
|
| City |
Norman |
| State/province |
Oklahoma |
| ZIP/Postal code |
73069 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE131649 |
ARID3a is Required for Erythrocyte Lineage Differentiation of Hemin Stimulated Human K562 Cells |
|
| Relations |
| BioSample |
SAMN15661073 |
| SRA |
SRX8840281 |
