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Sample GSM7734083 Query DataSets for GSM7734083
Status Public on Mar 13, 2024
Title BAC-Igf2_Igf2_Sox2DistalLCR~miICR-BS11125A
Sample type SRA
 
Source name BAC clone library
Organism synthetic construct
Characteristics cell type: None
payload id: Igf2_Igf2_Sox2DistalLCR~miICR
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 SAMN37148633
SRA SRX21482139

Supplementary file Size Download File type/resource
GSM7734083_BAC-Igf2_Igf2_Sox2DistalLCR_miICR-BS11125A.mm10.coverage.bw 1018.0 Kb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA

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