|
| Status |
Public on Aug 01, 2018 |
| Title |
ES8: END_seq_aHCT116_8h_HU_8h_10mM_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
HCT116
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: HCT116
genotype: WT
strain: N/A
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Single cell suspensions of B-cells (15 million per agarose plug), T-cells (15 million per agarose plug), MEFS (4 million per agarose plug), HCT116 (7.5 million per agarose plug)were washed in PBS, embedded in agarose and transferred into plug molds (Bio-Rad CHEF Mammalian Genomic DNA plug kit) and processed as previously described (Canela et al., 2016). Libraries were quantified using with the KAPA Library Quantification Kit (Kapa Biosciences) and sequenced in a NextSeq 550 system (Illumina, 75 bp single end reads).
libraries were prepared and sequenced following standard Illumina protocols
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
NextSeq 550 |
| |
|
| Description |
Control: END_seq_aHCT116_8h_NT_rep1
|
| Data processing |
Library strategy: END-seq
mouse and human reads were aligned to the GRCm38p2/mm10 and GRCh37/hg19 genome assemblies,respectively.
Alignment done using bowtie version 0.12.7, with the parameters: -l 25 -n 3 --best --all --strata -M 1 --tryhard –t
END-seq peaks were called using the parameters: --nolambda,-- nomodel and –keep-dup=all
Genome_build: GRCm38p2/mm10 for mouse and GRCh37/hg19 for human
Supplementary_files_format_and_content: bigwig files were made using Bedtools genomecov function followed by UCSC toolkit function bedGraphToBigWig
|
| |
|
| Submission date |
Jun 27, 2018 |
| Last update date |
Aug 01, 2018 |
| Contact name |
Andre Nussenzweig |
| E-mail(s) |
[email protected]
|
| Organization name |
National Institutes of Health
|
| Department |
National Cancer Institute
|
| Lab |
Laboratory of Genome Integrity
|
| Street address |
9000 Rockville Pike, Building 37
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL21697 |
| Series (2) |
| GSE116315 |
END-seq profile in B,T, and HCT116 untreated and upon HU treatment |
| GSE116321 |
Dual Roles of Poly(dA:dT) Tracts in Replication Initiation and Fork Collapse |
|
| Relations |
| BioSample |
SAMN09499673 |
| SRA |
SRX4310943 |
