|
| Status |
Public on Nov 27, 2023 |
| Title |
AG04441 early passage with ex527 replicate 2 |
| Sample type |
SRA |
| |
|
| Source name |
Skin
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Skin
cell line: AG04441
cell type: Human skin fibroblast
treatment: early passage with ex527
|
| Biomaterial provider |
Coriell Cell Repositories https://catalog.coriell.org/0/Sections/Search/Sample_Detail.aspx?Ref=AG04441
|
| Treatment protocol |
Fibroblast cells were immortalized by human Telomerase Reverse Transcriptase protein (hTERT). Cells were then cultured on a cover glass and treated with and without EX527 (1uM for 48hr). The SIRT1 gene was deleted from the cancer cell lines using CRISPR-Cas9 targeting exon1.
|
| Growth protocol |
Fibroblasts were grown in MEM medium, 15% FBS
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA from cell cultures was isolated, size fractionated and subject to exonuclease digestion as described in Aladjem et al., Science 281, 1005, 1998. and Wang et al., Molecular and Cellular Biology 24:3373-86, 2004. For ChipSeq, DNA molecules were enriched using antibodies against proteins of interest.
Samples were eluted, and then purified by Monarch PCR & DNA Cleanup Kit (NEBT1030S). 100 ng of NS samples were used to generate the library. The kits used for the library were NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7805S) and NEBNext Multiplex Oligos for Il-lumina (Index Primers Set 1 and Set 2) (NEB, E7335S and E7500S).
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
BAM files were filtered using alignmentSieve to remove reads shorter than 40bp
For nascent strand peak calling the MACS2 algorithm was used.
Nascent strand reads were called by comparison to genomic DNA.
Peaks were filtered to accept the top 40% by q-value based on the raw output
Assembly: T2T
Supplementary files format and content: Bed file format of replication origin peaks
Supplementary files format and content: BigWig file format of replication origin locations
Library strategy: NS-seq
|
| |
|
| Submission date |
Nov 10, 2023 |
| Last update date |
Nov 27, 2023 |
| Contact name |
Christophe E Redon |
| E-mail(s) |
redonc@mail.nih.gov
|
| Phone |
240-760-7338
|
| Organization name |
NIH
|
| Street address |
37 Convent Drive
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE247469 |
SIRT1 prevents R-loops during chronological aging by modulating DNA replication at rDNA loci |
|
| Relations |
| BioSample |
SAMN38199662 |
| SRA |
SRX22482520 |
