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| Status |
Public on Mar 31, 2023 |
| Title |
Trio-109_father-130 |
| Sample type |
SRA |
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| Source name |
blood
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| Organism |
Homo sapiens |
| Characteristics |
tissue: blood
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was purified using the QIAamp DNA Blood Mini Kit (Qiagen) following the manufacturer’s instructions.
Multiplexed Illumina libraries were prepared using the KAPA Library Preparation Kit (NimbleGen) following the manufacture’s instruction; we used Illumina adapters from the SeqCap Adapter Kit (NimbleGen)
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
Library strategy: RC-seq (Retrotransposon Capture Sequencing)
Computational analysis of reads was implemented according to the RC-seq pipeline described by Shuckla et al. (Shukla et al., 2013). Briefly, the RC-seq pipeline is conducted to search for split reads that represent a L1-insertion junction, being constituted by an L1-end and a flanking DNA sequence. Flanking DNA sequences are aligned to the Human Genome Reference Sequence (hg19) using SOAP (Li et al., 2009) (parameters –M 4 –v 2 –r 1 –p 8) and the L1-end characterized by mapping to the human active L1 consensus sequences (L1Hs-Ta/L1Hs-preTa) using LAST (Kielbasa et al., 2011) (parameters –s 2 –l 11 –d 30 –q 3 –e 30) (alignment at >95% identity and spanning at least 33 nucleotides of the read end). To assess the reliability of RC-seq, we determined the percentage of L1Hs copies annotated in hg19 (available from euL1db at http://eul1db.unice.fr/, contains 1544 reference L1Hs copies annotated) that were detected by RC-seq in the different WGA-gDNA samples. As an additional control, we also compared recovered insertions in H9-hESCs and hEMBs with the L1Hs-Ta subset of reference L1Hs (485 copies). Finally, L1-insertions were further filtered with respect to reference L1-insertions annotated in hg19 and to reported polymorphic L1-insertions (from euL1db database (Mir et al., 2015) and from recent publications not included yet in this database (Tubio et al., 2014)).
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| Submission date |
Apr 27, 2020 |
| Last update date |
Mar 31, 2023 |
| Contact name |
Martin Munoz-Lopez |
| E-mail(s) |
martin.munoz.science@gmail.com
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| Organization name |
GENYO
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| Street address |
C/ Ilustración
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| City |
Granada |
| State/province |
GRANADA |
| ZIP/Postal code |
18016 |
| Country |
Spain |
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| Platform ID |
GPL18573 |
| Series (2) |
| GSE149475 |
LINE-1 retrotransposition impacts the genome of human pre-implantation embryos and extraembryonic tissues [trios] |
| GSE149477 |
LINE-1 retrotransposition impacts the genome of human pre-implantation embryos and extraembryonic tissues |
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| Relations |
| BioSample |
SAMN14749936 |
| SRA |
SRX8183727 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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