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| Status |
Public on Sep 26, 2023 |
| Title |
Isoform-resolved transcriptome of the human preimplantation embryo [PacBio] |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Human preimplantation development is a complex process involving extensive remodeling of gene expression. However, the preimplantation embryo transcriptome has only been annotated using short-read sequencing, which fails to capture full-length mRNAs and associated isoform diversity. We present a novel human embryo transcriptome using integrated long- and short-read RNA sequencing data. Our analysis reveals a total of 110,212 novel isoforms transcribed from known genes containing either a novel combination of known splice sites or at least one novel splice site, and 17,964 isoforms transcribed from completely novel genes located either in antisense direction of known genes or in intergenic space.
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| Overall design |
RNA sequencing data was generated from a total of 73 human embryos across six pre-implantation stages: 13 zygotes (1C), 13 2-cell (2C) embryos, 16 4-cell (4C) embryos, 15 8-cell (8C) embryos, 3 morulae and 13 blastocysts. For each embryo, mRNA was extracted and converted to full-length cDNA, and used to generate Illumina RNA-Seq data, generating an average of 58.6 million paired end reads per sample. The same cDNA samples were used for SMRT-seq, pooling together low-yield samples to obtain enough mass for long-read sequencing. This resulted in a total of 10,139,308 full-length nonchimeric (FLNC) reads across 10 Sequel II SMRTcells, with an average cDNA length of 1,332 bp.
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| Contributor(s) |
Torre D, Francoeur N, Kalma Y, Ben-Yosef D, Sebra R |
| Citation(s) |
37903791 |
| Submission date |
Dec 09, 2021 |
| Last update date |
Nov 16, 2023 |
| Contact name |
Robert Sebra |
| E-mail(s) |
robert.sebra@mssm.edu
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| Organization name |
Icahn School of Medicine at Mount Sinai
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| Street address |
1 Gustave L. Levy Place
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| City |
New York |
| State/province |
New York |
| ZIP/Postal code |
10029 |
| Country |
USA |
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| Platforms (1) |
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| Samples (10)
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| This SubSeries is part of SuperSeries: |
| GSE190548 |
Isoform-resolved transcriptome of the human preimplantation embryo |
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| Relations |
| BioProject |
PRJNA787547 |
| SRA |
SRP350000 |
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