NYU Data Catalog

NYU Dataset

Transposon Insertion Profiling by Sequencing (TIPseq) Utilized for LINE-1 Mapping in Single Cells

Part of: Fenyo Lab |
UID: 10460
Author(s): Wilson McKerrow, Zuojian Tang, Jared P. Steranka, Lindsay M. Payer, Jef D. Boeke...
* Corresponding Author
Description

This dataset was compiled to determine a genome-wide long interspersed element-1 (LINE-1) insertion site mapping method for bulk DNA. This study has shown that transposon insertion profiling by sequencing (TIPseq) is a method that can be used for LINE-1 mapping in single cells. Live GM12878 lymphoblastoid cells were used for this study. The dataset contains sequencing data as well as supplementary data tied to the publication. Supplementary data includes data for primers for quality control qPCR and multiple displacement amplification or multiple annealing and looping-based amplification cycles, which was used to perform single-cell whole-genome amplification.

Subject of Study
GM12878 cells
Subject Domain
Genomics
Keywords
DNA
Epigenetics
Genes
Genomics
Human Genome
Proteins
Retrotransposons
Whole Genome Sequencing

Access

Restrictions
Free to All
Instructions
All the sequencing data are deposited at Sequence Read Archive (SRA) with BioProject. The analyzed data supporting this article are present on PubMed Central (PMC) under Supplementary Material.
Access via SRA

Sequencing data
Accession #: PRJNA547805

Access via PMC

Analyzed data
Accession #: PMC7061987

Associated Publications
McKerrow W, Tang Z, Steranka JP, Payer LM, Boeke JD, Keefe D, Fenyö D, Burns KH, Liu C. Human transposon insertion profiling by sequencing (TIPseq) to map LINE-1 insertions in single cells. Philos Trans R Soc Lond B Biol Sci. 2020 Mar 30;375(1795):20190335. doi: 10.1098/rstb.2019.0335. Epub 2020 Feb 10. PMID: 32075555; PMCID: PMC7061987.
Data Type
Genomic
Equipment Used
Illumina HiSeq 4000

Sequencing system

Software Used
TIPseqHunter2

Genome assembly (Java and R)

Grant Support
R01 GM124531/NIGMS NIH
P01 AG051449/NIA NIH