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TranscriptomicsA comprehensive map of L1HS-Ta retrotransposons in a panel of human cells obtained by ATLAS-seq.
We used ATLAS-seq to comprehensively map the genomic location of LINE-1 elements belonging to the youngest and potentially polymorphic subfamily (L1HS-Ta). This was performed in a panel of 12 human primary or transformed cell lines (BJ, IMR90, MRC5, H1, K562, HCT116, HeLa S3, HepG2, MCF7, HEK-293, H...
ORGANISM(S): Homo sapiens 
2016-05-24 | E-MTAB-4676 | biostudies-arrayexpress
TranscriptomicsRNA-seq of MCF-7 (breast adenocarcinoma) and 2102Ep (embryonic carcinoma) cells upon LINE-1 knockdown.
To measure the levels of expression of retrotransposon individual copies, and particularly of LINE-1 (L1) elements of the L1HS-Ta subfamily, we performed 2x150 bp paired-end and strand-specific RNA-seq on polyA+ RNA of MCF-7 and 2102Ep cells, which express high levels of L1. To confirm the origin of...
ORGANISM(S): Homo sapiens 
2016-05-25 | E-MTAB-3788 | biostudies-arrayexpress
TranscriptomicsIdentification of de novo LINE-1 (L1) retrotransposon integration sites in HeLa S3 cells by ATLAS-seq-neo (unselected insertions)
We used ATLAS-seq-neo to map the sites of integration of an engineered LINE-1 (L1) retrotransposon into the genome of HeLa S3 cells. In brief, we transfected cells with a plasmid-borne L1.3 element carrying a neomycin-resistance-based retrotransposition cassette, as well as a hygromycin-resistance c...
ORGANISM(S): Homo sapiens 
2019-04-03 | E-MTAB-7644 | biostudies-arrayexpress
TranscriptomicsSingle-cell identification of L1HS-Ta retrotransposons in preimplantation embryos by ATLAS-seq
We used ATLAS-seq to comprehensively map the genomic location of LINE-1 elements belonging to the youngest and potentially polymorphic subfamily (L1HS-Ta). This was performed in single-cells of 2 preimplantation embryos (E3 and E6) as well as from the remaining inner cell mass (denoted T). In brief,...
ORGANISM(S): Homo sapiens 
2023-09-30 | E-MTAB-8616 | biostudies-arrayexpress
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