Homo sapiens
Protocols: Cells were transfected with a plasmid-borne L1.3 element carrying a NeoR-based retrotransposition cassette and a hygromycin-resistance gene in the vector backbone. Transfected cells were selected with hygromycin (but not by G418) for 10 days. Genomic DNA was extracted using a QiaAmp DNA Blood mini kit (Qiagen). ATLAS-seq-neo libraries were prepared by random mechanical fragmentation of the genomic DNA to ensure high-coverage, ligation of adapter sequences, and suppression PCR-amplification of the 3' end L1 junction with its flanking genomic sequence. The primers used for suppression PCR specifically targets the engineered element and not endogenous copies as in the original ATLAS-seq protocol (Philippe et al. eLife 2016), and are fused to Ion Torrent-specific A and trP1 primers. Libraries are oriented with reads directed from the flanking sequence to the L1 3' end (reads have the following structure: 5'-A-barcode-linker-flank-poly(dT)-L1-trP1-3'). This library construction protocol used suppression PCR reactions performed in solution.
ENA-FIRST-PUBLIC
2019-04-03T13:14:34Z
ENA-LAST-UPDATE
2019-02-01T16:10:30Z
External Id
SAMEA5315632
INSDC center name
Universite Cote d'Azur, Inserm, CNRS
INSDC first public
2019-04-03T13:14:34Z
INSDC last update
2019-02-01T16:10:30Z
INSDC status
public
Submitter Id
E-MTAB-7644:SH03
broker name
ArrayExpress
cell line
HeLa-S3
common name
human
growth condition
Hygromycin
replicate
3
sample name
E-MTAB-7644:SH03
scientific_name
Homo sapiens
sex
female