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Status |
Public on Mar 13, 2024 |
Title |
BAC-Igf2_Igf2_miICR~Igf2SV-BS08664A |
Sample type |
SRA |
|
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Source name |
BAC clone library
|
Organism |
synthetic construct |
Characteristics |
cell type: None payload id: Igf2_Igf2_miICR~Igf2SV 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)
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Library strategy |
OTHER |
Library source |
genomic |
Library selection |
other |
Instrument model |
NextSeq 550 |
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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)
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|
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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 |
SAMN37148639 |
SRA |
SRX21482133 |