|
|
GEO help: Mouse over screen elements for information. |
|
Status |
Public on Mar 31, 2023 |
Title |
E3.C3 |
Sample type |
SRA |
|
|
Source name |
blastocyst
|
Organism |
Homo sapiens |
Characteristics |
tissue: blastocyst developmental stage: day +6 origin: single-cell embryo: embryo_3
|
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)
|
|
|
Library strategy |
OTHER |
Library source |
genomic |
Library selection |
other |
Instrument model |
Illumina HiSeq 2500 |
|
|
Description |
whole genome amplification Multiple Displacement Amplification
|
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)).
|
|
|
Submission date |
Apr 27, 2020 |
Last update date |
Mar 31, 2023 |
Contact name |
Martin Munoz-Lopez |
E-mail(s) |
martin.munoz.science@gmail.com
|
Organization name |
GENYO
|
Street address |
C/ Ilustración
|
City |
Granada |
State/province |
GRANADA |
ZIP/Postal code |
18016 |
Country |
Spain |
|
|
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 |
|
Relations |
BioSample |
SAMN14749922 |
SRA |
SRX8183685 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
|
|
|
|
|