|
| Status |
Public on Feb 18, 2019 |
| Title |
Input |
| Sample type |
SRA |
| |
|
| Source name |
HeLa cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HeLa
chromation digestion: Sonication
treatment: none
|
| Treatment protocol |
Two million cells were used to purify chromatin according the REAP protocol (Sizuki et al. 2010) and digested with 5 to 30 units of Dnase I for 5 minutes at 25°C.
|
| Growth protocol |
HeLa cells were grown on DMEM-Dubelco´s modified Eagle Medium containing Glutamax (TM from Gibco) supplemented with 10% Fetal Bovine serum, and maintained at 37°C with 5% CO2.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Samples were treated with RNase A and Proteinase K prior to DNA extraction with phenol-chloroform-isoamylalcohol.
Libraries were prepared according to NEBNext ChIP-Seq Kit for Illumina sequencing. Adapter were removed by size selection using AMPure XP magnetic beads.
|
| |
|
| Library strategy |
DNase-Hypersensitivity |
| Library source |
genomic |
| Library selection |
DNAse |
| Instrument model |
NextSeq 550 |
| |
|
| Data processing |
Library strategy: DNase-seq
Paired-end reads were aligned to hg19 assembly using bowtie2 version 2.2.2 with the following configurations: --very-sensitive-local --no-discordant -X 2000
Aligned reads exhibiting a mapping quality MAPQ < 30 were discarded using samtools version 1.1
Genome_build: hg19
Supplementary_files_format_and_content: biwig files were generated using the bamCoverage script from the deepTools package (--extendReads -binSize 1 ) and show the normalized (--normalizeTo1x 2451960000) genome coverage
|
| |
|
| Submission date |
May 24, 2018 |
| Last update date |
Feb 18, 2019 |
| Contact name |
Uwe Schwartz |
| E-mail(s) |
uwe.schwartz@ur.de
|
| Organization name |
University of Regensburg
|
| Department |
NGS Analysis Center
|
| Street address |
Universitätstraße 32
|
| City |
Regensburg |
| ZIP/Postal code |
93053 |
| Country |
Germany |
| |
|
| Platform ID |
GPL21697 |
| Series (1) |
| GSE114900 |
Nucleosomes stabilize ssRNA-dsDNA triple helices in human cells |
|
| Relations |
| BioSample |
SAMN09257993 |
| SRA |
SRX4123094 |
