|
| Status |
Public on Oct 30, 2024 |
| Title |
LF1 cells, proliferating, replicate 1 |
| Sample type |
SRA |
| |
|
| Source name |
LF1
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: LF1
cell type: lung fibroblasts
genotype: WT
treatment: None
|
| Treatment protocol |
Proliferating cells were harvested at 60 - 80% confluency.
Replicative senescent (RS) cells were passaged in regular growth media until replicative exhaustion. These cells were maintained in the senescent state for 3-4 months.
|
| Growth protocol |
Cells were passaged in regular growth media (HAMS F10, 15% FBS, and 1x of Penicillin Streptomycin and Glutamine) and maintained at 37 degrees Celsius at 5% CO2 and 2.5% O2.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
All conditions (proliferating, quiescent, RS) had genomic DNA extracted using the Monarch genomic DNA purification kit from NEB. The standard protocol for DNA extraction from cells was followed with no modifications.
Sequencing libraries were prepared using the Oxford Nanopore Ligation Sequencing Kit V14 and its associated protocol. Long-fragment buffer was used to enrich for long DNA fragments.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
PromethION |
| |
|
| Data processing |
>60X coverage worth of nanopore long sequencing reads were fed to the “TLDR” program
Extra chromosomal insertion “patches” were appended to the T2T-HS1 reference, which were comprised of the full private insert sequence plus 500 base pairs of flanking sequence on either side of the insert-breakpoint.
Custom gene transfer file annotations were subsequently produced to document the presence of these private insertions. All reference and private L1HS and L1PA2 elements were inspected for the presence of intact (full length ORF1p and ORF2p) protein coding potential.
Sequences were extracted from our custom reference using bedtools getfasta in addition to the private insert augmented T2T-HS1 RepeatMasker gtf annotation. Open reading frames were detected using the R package “Orfik” and filtered on the basis of length. Elements which passed these criteria were denoted as “intact”.
Reference and private intact L1HS coordinates were lifted over to hg38 with the liftOver tool from the Broad Institute for use in Hi-C analyses which had reads aligned to this reference.
Assembly: hg38
Supplementary files format and content: list of L1 reference and novel
Library strategy: Long read DNA-Seq
|
| |
|
| Submission date |
May 28, 2024 |
| Last update date |
Oct 30, 2024 |
| Contact name |
Nicola Neretti |
| E-mail(s) |
[email protected]
|
| Organization name |
Brown University
|
| Street address |
225 Dyer St.
|
| City |
Providence |
| State/province |
RI |
| ZIP/Postal code |
02903 |
| Country |
USA |
| |
|
| Platform ID |
GPL26167 |
| Series (1) |
| GSE268488 |
High-resolution Hi-C reveals increased chromatin looping with senescence associated with hypomethylation and retrotransposon derepression [Long Read DNA-seq] |
|
| Relations |
| BioSample |
SAMN41570217 |
| SRA |
SRX24725662 |
