|
| Status |
Public on Jan 14, 2021 |
| Title |
H1-PL1-B6-BS06872A |
| Sample type |
SRA |
| |
|
| Source name |
BS06872A
|
| Organism |
Homo sapiens |
| Characteristics |
strain: n/a
age: n/a
genotype: delta-HPRT1,LP-TK[HPRT1],PL1[LP-TK]
cell line: H1-hESC
treatment: None
|
| Treatment protocol |
Cells were selected combinatorially with puromycin, blasticidin, proaerolysin and ganciclovir as described in the manuscript
|
| Growth protocol |
hESCs were grown on Geltrex-coated plates with StemFlex medium supplemented with 1% Pen-Strep and passaged in clumps using Versene. mESCs were cultured on gelatin-coated plates coated in 80/20 medium comprising 80% 2i medium and 20% mESC medium and with 1% Pen-strep.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were dissociated using TryPE-Select, spun-down and media aspirate. Pellets were either processed immediately or stored at -80 deg. Genomic DNA was extracted using the DNeasy Blood & Tissue kit (QIAGEN 69506).
Double-stranded DNA libraries were prepared from sheared genomic DNA. DNA fragments were end-repaired, A-tailed, and Illumina-compatible adapters were ligated to DNA ends.
Other - DNA Capture-seq
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Captured genomic DNA
|
| Data processing |
Illumina libraries were sequenced in paired-end mode on an Illumina NextSeq 500 operated at the Institute for Systems Genetics or NovaSeq 6000 operated by the NYU Langone Health Genome Technology Center. Reads were demultiplexed with Illumina bcl2fastq v2.20 requiring a perfect match to indexing BC sequences. All WGS and Capture-Seq data were processed using a uniform mapping and peak calling pipeline. Illumina sequencing adapters were trimmed with Trimmomatic v0.39{Bolger, 2014 #3524}. Sequencing reads were aligned using BWA v0.7.17{Li, 2009 #3526} to a genome reference (GRCh38/hg38 or GRCm38/mm10) including unscaffolded contigs and alternate references, as well as independently to custom references for relevant vectors and their payloads. PCR duplicates were marked using samblaster v0.1.24{Faust, 2014 #3527}. Generation of per-base coverage depth tracks and quantification was performed using BEDOPS v2.4.35{Neph, 2012 #3540}. Data were visualized using the UCSC Genome Browser. The sequencing processing pipeline is available at https://github.com/mauranolab/mapping .
Genome_build: mm10 and hg38
Supplementary_files_format_and_content: coverage depth track (bigwig)
|
| |
|
| Submission date |
Oct 13, 2020 |
| Last update date |
Jan 15, 2021 |
| Contact name |
Mathew T Maurano |
| E-mail(s) |
maurano@nyu.edu
|
| Organization name |
NYU Langone Health
|
| Department |
Institute for Systems Genetics
|
| Lab |
Maurano Lab
|
| Street address |
435 E 30th St
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10016 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE159488 |
A versatile platform for locus-scale genome rewriting and verification |
|
| Relations |
| BioSample |
SAMN16431869 |
| SRA |
SRX9287948 |
