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| Status |
Public on Mar 31, 2023 |
| Title |
E6.C3 |
| Sample type |
SRA |
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| Source name |
blastocyst
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| Organism |
Homo sapiens |
| Characteristics |
tissue: blastocyst
developmental stage: day +5
origin: single-cell
embryo: embryo_6
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Whole Genome Aamplification reactions were performed within 48 hours after single-cell extraction, using the GenomiPhi v2 DNA Amplification Kit (GE Healthcare)
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 HiSeq 2500 |
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| Description |
whole genome amplification
Multiple Displacement Amplification
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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 |
GPL16791 |
| Series (2) |
| GSE149472 |
LINE-1 retrotransposition impacts the genome of human pre-implantation embryos and extraembryonic tissues [hEMB] |
| GSE149477 |
LINE-1 retrotransposition impacts the genome of human pre-implantation embryos and extraembryonic tissues |
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| Relations |
| BioSample |
SAMN14749918 |
| SRA |
SRX8183690 |
| 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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