|
| Status |
Public on Mar 13, 2024 |
| Title |
BAC-Sox2_DistalLCR_H19enh~inverted-BS11098A |
| Sample type |
SRA |
| |
|
| Source name |
BAC clone library
|
| Organism |
synthetic construct |
| Characteristics |
cell type: None
payload id: Sox2_DistalLCR_H19enh~inverted
seq method: payload sequencing
|
| Treatment protocol |
Cells were engineered with different landing pads and payloads as described and were selected combinatorially with puromycin, blasticidin, proaerolysin and ganciclovir as described in the manuscript.
|
| Growth protocol |
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.
Payload and Targeted sequencing (Capture-seq)
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
NextSeq 550 |
| |
|
| Data processing |
Illumina libraries were sequenced in paired-end mode on an Illumina NextSeq 500 operated at the Institute for Systems Genetics. 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. Sequencing reads were aligned using BWA v0.7.17 to a genome reference (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. Generation of per-base coverage depth tracks and quantification was performed using BEDOPS v2.4.35.
The sequencing processing pipeline is available at https://github.com/mauranolab/mapping .
Assembly: mm10
Supplementary files format and content: coverage bigwig files for captured genomic DNA libraries to genome reference (GRCm38/mm10)
|
| |
|
| Submission date |
Aug 24, 2023 |
| Last update date |
Mar 13, 2024 |
| Contact name |
Matthew T Maurano |
| Organization name |
NYU Grossman School of Medicine
|
| Department |
Institute for Systems Genetics
|
| Lab |
Maurano lab
|
| Street address |
435 East 30th Street
|
| City |
New York |
| State/province |
New York |
| ZIP/Postal code |
10016 |
| Country |
USA |
| |
|
| Platform ID |
GPL27609 |
| Series (2) |
| GSE241706 |
Genomic context sensitizes regulatory elements to genetic disruption [DNA] |
| GSE241708 |
Genomic context sensitizes regulatory elements to genetic disruption |
|
| Relations |
| BioSample |
SAMN37148636 |
| SRA |
SRX21482136 |
