Produce dataset of EST to design probes and a new microarray platform |
Robert et al. (2011)Robert C, Nieminen J, Dufort I, Gagné D, Grant JR, Cagnone G, Plourde D, Nivet A, Fournier É, Paquet É, Blazejczyk M, Rigault P, Juge N, Sirard M. 2011. Combining resources to obtain a comprehensive survey of the bovine embryo transcriptome through deep sequencing and microarrays. Mol Reprod Dev, 78:651-664.
|
Bovine |
Genome Sequencer FLX, 454 Life Sciences |
Sequencing of germinal vesicle oocyte, 2-, 4-, 8-, 16-cells, morula, blastocyst and hatched blastocyst produced in vitro and derived in vivo
|
Tsoi et al. (2012)Tsoi S, Zhou C, Grant JR, Pasternak JA, Dobrinsky J, Rigault P, Nieminen J, Sirard MA, Robert C, Foxcroft GR, Dyck MK. 2012. Development of a porcine (Sus scofa) embryo-specific microarray: array annotation and validation. BMC Genomics, 3(13):370. Doi: 10.1186/1471-2164-13-370. https://doi.org/10.1186/1471-2164-13-370...
|
Porcine |
Genome Sequencer FLX, 454 Life Sciences |
Sequencing of germinal vesicle, metaphase II oocyte, 2-, 4-, 8-, morula, expanded and hatched blastocyst produced in vitro and derived in vivo
|
Study oocyte competence |
Macaulay et al. (2014)Macaulay AD, Gilbert I, Caballero J, Barreto R, Fournier E, Tossou P, Sirard MA, Clarke HJ, Khandjian ÉW, Richard FJ, Hyttel P, Robert C. 2014. The gametic synapse: RNA transfer to the bovine oocyte. Biol Reprod, 91(4):90. Doi: 10.1095/biolreprod.114.119867. https://doi.org/10.1095/biolreprod.114.1...
|
Bovine |
Illumina, HiSeq 2000 |
Comparison of germinal vesicle versus metaphase II oocytes matured in vitro
|
Reyes et al. (2015)Reyes JM, Chitwood JL, Ross PJ. 2015. RNA-Seq profiling of single bovine oocyte transcript abundance and its modulation by cytoplasmic polyadenylation. Mol Reprod Dev, 82(2):103-114.
|
Bovine |
Illumina, HiSeq 2000 |
Comparison of polyadenylated transcripts in germinal vesicle versus metaphase II oocytes matured in vitro
|
Macaulay et al. (2016)Macaulay AD, Gilbert I, Scantland S, Fournier E, Ashkar F, Bastien A, Saadi HA, Gagné D, Sirard MA, Khandjian ÉW, Richard FJ, Hyttel P, Robert C. 2016. Cumulus Cell Transcripts Transit to the Bovine Oocyte in Preparation for Maturation. Biol Reprod, 94(1):16. Doi: 10.1095/biolreprod.114.127571. https://doi.org/10.1095/biolreprod.114.1...
|
Bovine |
Illumina, HiSeq 2000 |
Comparison of germinal vesicle versus metaphase II oocytes in vitro matured versus total RNA found in the TZPs |
|
Gilchrist et al. (2016)Gilchrist GC, Tscherner A, Nalpathamkalam T, Merico D, LaMarre J. 2016. MicroRNA Expression during Bovine Oocyte Maturation and Fertilization. Int J Mol Sci, 17(3):396. Doi: 10.3390/ijms17030396. https://doi.org/10.3390/ijms17030396...
|
Bovine |
Illumina, HiSeq 2500 |
Comparison of germinal vesicle versus metaphase II oocytes versus presumptive zygotes |
Study non-invasive mRNA and miRNA biomarkers of oocyte competence |
Luo et al. (2016)Luo F, Jia R, Ying S, Wang Z, Wang F. 2016. Analysis of genes that influence sheep follicular development by different nutrition levels during the luteal phase using expression profiling. Anim Genet, 47(3):354-364.
|
Sheep |
Illumina, HiSeq 2000 |
Comparison of granulosa cells isolated from animals short-term dietary-restricted versus nutrient-supplemented |
Wu et al. (2017)Wu Y, Lin J, Li X, Han B, Wang L, Liu M, Huang J. 2017. Transcriptome profile of one-month-old lambs’ granulosa cells after superstimulation. Asian-Australas J Anim Sci, 30(1):20-33.
|
Sheep |
Illumina, HiSeq 2500 |
Comparison of granulosa cells isolated from prepubertal versus adult superstimulated follicles |
Mazzoni et al. (2017)Mazzoni G, Salleh SM, Freude K, Pedersen HS, Stroebech L, Callesen H, Hyttel P, Kadarmideen HN. 2017. Identification of potential biomarkers in donor cows for in vitro embryo production by granulosa cell transcriptomics. PLoS ONE, 12(4):e0175464.
|
Bovine |
Illumina, HiSeq 2500 |
Sequencing of granulosa cells collected at OPU prior to IVEP. Follow IVEP and correlation of the blastocyst rates with RNA-seq results |
Study transcriptomic profile and molecular markers of sperm quality |
Card et al. (2013)Card CJ, Anderson EJ, Zamberlan S, Krieger KE, Kaproth M, Sartini BL. 2013. Cryopreserved bovine spermatozoal transcript profile as revealed by high-throughput ribonucleic acid sequencing. Biology of Reproduction, 88(2):1-9.
|
Bovine |
Illumina, HiSeq 2000 |
Sequencing of cryopreserved spermatozoa |
Kropp et al. (2017)Kropp J, Carrillo JA, Namous H, Daniels A, Salih SM, Song J, Khatib H. 2017. Male fertility status is associated with DNA methylation signatures in sperm and transcriptomic profiles of bovine preimplantation embryos. BMC Genomics, 18(1):280. Doi: 10.1186/s12864-017-3673-y. https://doi.org/10.1186/s12864-017-3673-...
|
Bovine |
Illumina, HiSeq 2000 |
Comparison of blastocysts derived from low-fertility versus high-fertility bull (based on SCR) |
Selvaraju et al. (2017)Selvaraju S, Parthipan S, Somashekar L, Kolte AP, Krishnan Binsila B, Arangasamy A, Ravindra JP. 2017. Occurrence and functional significance of the transcriptome in bovine (Bos taurus) spermatozoa. Sci Rep, 7:42392.
|
Bovine |
Ion ProtonTM and Illumina, HiSeq 2000 |
Use of two NGS platafforms to sequence spermatozoa cells obtained from fresh semen |
Gòdia et al. (2018)Gòdia M, Mayer FQ, Nafissi J, Castelló A, Rodríguez-Gil JE, Sánchez A, Clop A. 2018. A technical assessment of the porcine ejaculated spermatozoa for a sperm-specific RNA-seq analysis. Syst Biol Reprod Med, 26:1-13.
|
Porcine |
Illumina, HiSeq 2000 |
Optimization of methodological workflow for RNA-seq of spermatozoa from fresh semen |
Study the onset of EGA |
Ostrup et al. (2013) |
Porcine |
SOLiD, Applied Biosystems |
Comparison of 2- and 4-cells embryos in vitro produced versus in vivo derived |
Graf et al. (2014)Graf A, Krebs S, Zakhartchenko V, Schwalb B, Blum H, Wolf E. 2014. Fine mapping of genome activation in bovine embryos by RNA sequencing. Proc Natl Acad Sci U S A, 111(11):4139-4144.
|
Bovine |
Illumina, GAIIx |
Comparison of germinal vesicle oocyte, metaphase II oocyte, 4-, 8-, 16-cells and blastocysts produced in vitro
|
Jiang et al. (2014)Jiang Z, Sun J, Dong H, Luo O, Zheng X, Obergfell C, Tang Y, Bi J, O'Neill R, Ruan Y, Chen J, Tian X. 2014. Transcriptional profiles of bovine in vivo pre-implantation development. BMC Genomics, 15(1):756. Doi: 10.1186/1471-2164-15-756. https://doi.org/10.1186/1471-2164-15-756...
|
Bovine |
SOLiD, Applied Biosystems |
Comparison of metaphase II oocyte, 2-, 4-, 8-, 16-cells, early morula, late morula and blastocyst derived in vivo
|
Jiang et al. (2015)Jiang Z, Dong H, Zheng X, Marjani SL, Donovan DM, Chen J, Tian XC. 2015. mRNA Levels of Imprinted Genes in Bovine In Vivo Oocytes, Embryos and Cross Species Comparisons with Humans, Mice and Pigs. Sci Rep, 5:17898. Doi:10.1038/srep17898. https://doi.org/10.1038/srep17898...
|
Bovine, human, mice and pig |
RNA-seq data downloaded from online database |
Comparison of metaphase II oocyte, 2-, 4-, 8-, 16-cells, early morula, late morula and blastocyst derived in vivo
|
Study the IVF effects on embryo development |
Bauer et al. (2010)Bauer BK, Isom SC, Spate LD, Whitworth KM, Spollen WG, Blake SM, Springer GK, Murphy CN, Prather RS. 2010. Transcriptional Profiling by Deep Sequencing Identifies Differences in mRNA Transcript Abundance in In Vivo-Derived Versus In Vitro-Cultured Porcine Blastocyst Stage Embryos. Biol Reprod, 83(5):791-798.
|
Porcine |
Illumina, GAIIx |
Comparison of blastocysts in vivo derived versus collected from uterus at 2-4-cells further in vitro cultured until blastocyst stage |
Huang and Khatib (2010)Huang W, Khatib H. 2010. Comparison of transcriptomic landscapes of bovine embryos using RNA-Seq. BMC Genomics, 11(1):711. Doi: 10.1186/1471-2164-11-711. https://doi.org/10.1186/1471-2164-11-711...
|
Bovine |
Illumina, GAIIx |
Comparison of fully developed in vitro blastocyst versus arrested embryos (failed to develop from morula to blastocyst stage) |
Redel et al. (2012)Redel BK, Brown AN, Spate LD, Whitworth KM, Green JA, Prather RS. 2012. Glycolysis in preimplantation development is partially controlled by the Warburg Effect. Mol Reprod Dev, 79(4):262-271.
|
Porcine |
Illumina, GAIIx |
Comparison of embryos in vitro cultured in low or high O2 atmospheres |
Driver et al. (2012)Driver AM, Penagaricano F, Huang W, Ahmad KR, Hackbart KS, Witlbank MC, Khatib H. 2012. RNA-Seq analysis uncovers transcriptomic variations between morphologically similar in vivo- and in vitro-derived bovine blastocysts. BMC Genomics, 13(1):118.
|
Bovine |
Illumina, Hiseq 2000 |
Comparison of in vitro and in vivo blastocysts with similar quality grade |
Cao et al. (2014)Cao S, Han J, Wu J, Li Q, Liu S, Zhang W, Pei Y, Ruan X, Liu Z, Wang X, Lim B, Ning L. 2014. Specific gene-regulation networks during the pre-implantation development of the pig embryo as revealed by deep sequencing. BMC Genomics, 15:4. Doi.org/10.1186/1471-2164-15-4. https://doi.org/Doi.org/10.1186/1471-216...
|
Porcine |
SOLiD 4, Applied Biosystems |
Comparison of 1-, 2-, 4-, 8-cells, morula and blastocysts in vivo derived versus produced in vitro using SCNT biotechnology |
Hera et al. (2016)Heras S, De Coninck DIM, Van Poucke M, Goossens K, Bogado Pascottini O, Van Nieuwerburgh F, Deforce D, De Sutter P, Leroy JLMR, Gutierrez-Adan A, Peelman L, Van Soom A. 2016. Suboptimal culture conditions induce more deviations in gene expression in male than female bovine blastocysts. BMC Genomics, 17:72. Doi: 10.1186/s12864-016-2393-z. https://doi.org/10.1186/s12864-016-2393-...
|
Bovine |
Illumina, HiSeq 2500 |
Comparison of blastocysts in vitro produced in serum-containing media versus serum free-media versus blastocysts derived in vivo
|
Milazzoto et al. (2016)Milazzotto MP, Goissis MD, Chitwood JL, Annes K, Soares CA, Ispada J, Assumpção ME, Ross PJ. 2016. Early cleavages influence the molecular and the metabolic pattern of individually cultured bovine blastocysts. Mol Reprod Dev, 83(4):324-336.
|
Bovine |
Illumina, HiSeq 2000 |
Comparison of slow and fast-cleavage embryos in vitro produced versus embryos derived in vivo
|
Study non-invasive mRNA and miRNA biomarkers of embryo quality |
Kropp et al. (2014)Kropp J, Salih SM, Khatib H. 2014. Expression of microRNAs in bovine and human pre-implantation embryo culture media. Front Genet, 5:91. Doi: 10.3389/fgene.2014.00091. https://doi.org/10.3389/fgene.2014.00091...
|
Bovine |
Illumina, GAIIx |
Comparison of media conditioned by fully developed blastocysts versus arrested embryos (failed to develop from morula to blastocyst) |
Kropp and Khatib (2015)Kropp J, Khatib H. 2015. mRNA fragments in in vitro culture media are associated with bovine preimplantation embryonic development. Front Genet, 6:273. Doi: 10.3389/fgene.2015.00273. https://doi.org/10.3389/fgene.2015.00273...
|
Bovine |
Illumina, GAIIx |
Comparison of media conditioned by fully developed blastocysts versus arrested embryos (failed to develop from morula to blastocyst) |