Microarray Analysis of Differentially Expressed Genes in Inner Cell Mass and Trophectoderm of Parthenogenetic Embryos

2016 ◽  
Vol 33 (1) ◽  
pp. 45-54
Author(s):  
Shiori Goto ◽  
Feng Cao ◽  
Tomohiro Kono ◽  
Hidehiko Ogawa
Keyword(s):  
Differentially Expressed Genes ◽  
Microarray Analysis ◽  
Inner Cell Mass ◽  
Cell Mass ◽  
Differentially Expressed ◽  
Parthenogenetic Embryos

205 RNA-SEq PROFILING OF BOVINE PRE-IMPLANTATION EMBRYOS

2013 ◽  
Vol 25 (1) ◽  
pp. 251
Author(s):  
S. Krebs ◽  
A. Graf ◽  
Z. Valeri ◽  
H. Blum ◽  
E. Wolf
Keyword(s):  
Differentially Expressed Genes ◽  
Developmental Stages ◽  
Inner Cell Mass ◽  
Cell Mass ◽  
Differentially Expressed ◽  
Rna Seq ◽  
Cell Stage ◽  
Total Rna ◽  
Genome Activation ◽  
Zygotic Genome

In order to provide a comprehensive view of the transcriptome changes during the earliest stages of bovine development, we sequenced the total RNA content of bovine oocytes, 4-cell, 8-cell, and 16-cell embryos and the inner cell mass and trophoblast envelope of expanded blastocysts on the Illumina Genome Analyzer IIx. For each experiment pools of in vitro matured oocytes from the German Simmental cows were fertilized by sperm of a single bull, and 10 oocytes or embryos per developmental stage were collected to generate total RNA pools used for sequencing. Synthesis of cDNA was initiated directly in the cell lysate in order to avoid any losses during RNA preparation and was random primed in order to capture all RNA species. Amplified cDNA and unstranded sequencing libraries were prepared using kits from Nugen (Ovation RNA-Seq, Nugen, San Carlos, CA, USA). Biological replicates were generated by inseminating the oocytes with sperm from the distant breeds Jersey (n = 3) and Brahman (n = 3). This cross-breeding design allowed tracking of single sequencing reads back to the maternal or paternal genome, where breed-specific SNP are present in the expressed transcripts. The analysis of this dataset resulted in monitoring of zygotic genome activation and parent-specific expression for single transcripts, a catalogue of splicing isoforms, novel transcripts, and non-coding RNAs and differentially expressed genes between the single developmental stages. Using the program DESEqn, 2784 genes showed differential expression between any of the stages at a false discovery rate of 1%. Specifically, we found 200 genes differentially expressed between immature and matured oocytes, 209 genes between matured oocytes and 4-cell embryos, 580 genes between the 4-cell and 8-cell stage, 567 genes between the 8-cell and 16-cell stage, 987 genes between the 16-cell stage and the inner cell mass, and 1569 genes between the 16-cell and the trophoblast. Functional analysis revealed stage-specific functions of the differentially expressed genes. In summary, by fully exploiting the single-nucleotide resolution of the RNA-Seq method, this dataset provides an invaluable resource for the study of zygotic genome activation, imprinting, transcript annotation, and gene expression in the earliest developmental stages of bovine embryos.

Identification of differentially expressed genes in human pineal parenchymal tumors by microarray analysis

2004 ◽  
Vol 109 (3) ◽  
pp. 306-313 ◽  
Author(s):  
Jacques Champier ◽  
Anne Jouvet ◽  
Catherine Rey ◽  
Virginie Brun ◽  
Arlette Bernard ◽  
...  
Keyword(s):  
Differentially Expressed Genes ◽  
Microarray Analysis ◽  
Differentially Expressed ◽  
Pineal Parenchymal Tumors

Defects in the allocation of cells to the inner cell mass and trophectoderm of parthenogenetic mouse blastocysts

1996 ◽  
Vol 8 (8) ◽  
pp. 1193 ◽  
Author(s):  
B Mognetti ◽  
D Sakkas
Keyword(s):  
Inner Cell Mass ◽  
Cell Mass ◽  
Substantial Reduction ◽  
Cell Lineage ◽  
Blastocyst Stage ◽  
Trophectoderm Cells ◽  
Parthenogenetic Development ◽  
Preimplantation Stage ◽  
Parthenogenetic Mouse Embryos ◽  
Parthenogenetic Embryos

Diploid parthenogenetic mouse embryos (which possess two maternally-derived genomes) can develop only as far as the 25-somite stage when transferred in utero and exhibit a substantial reduction in trophoblast tissue. The loss of cultured parthenogenetic embryos during postimplantation indicates that a defect in cell lineage may be evident as early as the blastocyst stage. The possibility that a defect may already be reflected at the preimplantation stage was investigated by examining the allocation of cells to the trophectoderm (trophoblast progenitor cells) and the inner cell mass of haploid and diploid parthenogenetic mouse blastocysts. Utilizing a differential labelling technique for counting cells, diploid parthenogenetic blastocysts were found to have fewer inner cell mass cells and trophectoderm cells than their haploid counterparts and normal blastocysts. In addition, both haploid and diploid parthenogenetic blastocysts had a lower inner cell mass: trophectoderm ratio than normal blastocysts. Thus, the relatively poor development of the trophectoderm lineage at the postimplantation stage is not reflected by a reduction in its allotment of cells at its first appearance. Nevertheless, the findings indicate that parthenogenetic development is already compromised at the blastocyst stage, and provide evidence that the expression of imprinted genes has significance for the development of the embryo at the preimplantation stage.

scholarly journals Microarray analysis of differentially expressed genes in the liver between Bai’er layers and broilers

2015 ◽  
Vol 14 (1) ◽  
pp. 2885-2889
Author(s):  
Q.-G. Wang ◽  
H.-F. Zhang ◽  
S.-Z. Wang ◽  
G.L. Gao ◽  
L. Leng ◽  
...  
Keyword(s):  
Differentially Expressed Genes ◽  
Microarray Analysis ◽  
Differentially Expressed

scholarly journals Cross platform microarray analysis for robust identification of differentially expressed genes

2007 ◽  
Vol 8 (S1) ◽  
Author(s):  
Roberta Bosotti ◽  
Giuseppe Locatelli ◽  
Sandra Healy ◽  
Emanuela Scacheri ◽  
Luca Sartori ◽  
...  
Keyword(s):  
Differentially Expressed Genes ◽  
Microarray Analysis ◽  
Differentially Expressed ◽  
Robust Identification ◽  
Cross Platform
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