RNA-seq of euploid versus aneuploid human embryo trophectoderm biopsies
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ABSTRACT:
PROVIDER: PRJEB55441 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR10089400_1.fastq.gz | Fastqsanger.gz | |||
| ERR10089400_2.fastq.gz | Fastqsanger.gz | |||
| ERR10089401_1.fastq.gz | Fastqsanger.gz | |||
| ERR10089401_2.fastq.gz | Fastqsanger.gz | |||
| ERR10089402_1.fastq.gz | Fastqsanger.gz |
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Project description:Embryos classified as euploid or aneuploid by PGT-A were re-biopsied and processed for RNA-Seq using a commercial kit (Takara Bio, USA, SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing) following the user manual. The resulting cDNAs were converted to libraries using a Nextera XT kit (Illumina, USA), with a modified protocol according to SMART-Seq v4 user manual. These libraries were pooled and sequenced using a NextSeq 550 instrument (Illumina, USA) with a MidOutput cartridge at 2x75 cycles. The sequencing reads in Fastq files were down-sampled to 6M total reads, aligned to the human genome assembly (hg38), and the number of transcripts per million (TPM) was determined using the CLC Genomics Workbench 12 (Qiagen, USA).
2022-09-07 | E-MTAB-12084 | biostudies-arrayexpress
Project description:Candida albicans lab strain SC5314, which is a euploid diploid, was used to generate aneuploid fluconazole adaptors. Transcriptomes of aneuploids were compared to the euploid parent by growing cells in rich YPD broth.
2022-09-26 | E-MTAB-12185 | biostudies-arrayexpress
Project description:Objective: To determine if embryos diagnosed as mosaic using Next-generation sequencing (NGS) have distinct gene expression profiles compared to embryos diagnosed as euploid or aneuploid. Materials and methods: Fifteen blastocysts were diagnosed as mosaic with NGS including 7 full mosaic monosomies, 5 partial mosaic monosomies, 2 full mosaic trisomies, and 1 partial mosaic trisomy. Three NGS diagnosed euploid embryos, and 25 aneuploid embryos (9 NGS, 14 aCGH, 2 Single Nucleotide Polymorphism array) were used as comparisons. Replicate samples were available for all euploid and full aneuploid embryos. Aneuploid embryos were chosen if their aneuploid chromosome corresponded with one of the mosaic embryos. Complementary DNA from the samples was created using the SMATer v4 Ultra Low Kit. RNA-seq library preparation followed by sequencing on the Illumina HiSeq 2500 with 50 nucleotide length paired end reads was performed. The STAR/2.5 aligner was used to align the reads against the hg19 ensemble reference transcriptome. Differentially expressed genes (DEGs) were calculated using DES-seq2/3.5, and p values <0.05 were considered significantly differentially expressed. Pathway analysis was performed on the top DEGs among all of the mosaic embryos with p<0.05 considered significant. Main results: The 15 mosaic embryos had transcriptomic profiles which were distinct from full aneuploid embryos involving the same chromosome. Mosaic embryos had fewer DEGs compared to aneuploid embryos of the same chromosome when using euploid embryos as controls. Mosaic embryos were grouped on principal component analysis (PCA) and distinguishable from euploid and aneuploid embryos. Pathways involving cell proliferation, differentiation, and apoptosis were the most disrupted from the presence of a mosaic cell line.
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Project description:We obtained ketoconazole tolerant mutants in Candida albicans after exposing the strain SC5314 to inhibitory concentration of ketoconazole. We did RNA-Seq to compare the transcriptomes of the aneuploid strains versus the parent euploid strain.
2020-03-30 | E-MTAB-8671 | biostudies-arrayexpress
Project description:Transcriptome analysis of aneuploid and euploid Candida albicans strains
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Project description:Comparative trancriptomes of aneuploid and euploid Candida glabrata strains
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Project description:Aneuploidy has been well documented in blastocyst embryos, but prior studies have been limited in scale and/or lack mechanistic data. We previously reported preclinical validation of microarray 24-chromosome preimplantation genetic screening (PGS) in a 24-hour protocol. The method diagnoses chromosome copy number, structural chromosome aberrations, parental source of aneuploidy, and distinguishes certain meiotic from mitotic errors. In this study our objective was to examine aneuploidy in human blastocysts and determine correspondence of karyotypes between trophectoderm (TE) and inner cell mass (ICM). We disaggregated 51 blastocysts from seventeen couples into ICM and one or two TE fractions. The average maternal age was 31. Next, we ran 24-chromosome microarray molecular karyotyping on all of the samples, and then performed a retrospective analysis of the data. The average per-chromosome confidence was 99.95%. Approximately 80% of blastocysts were euploid. The majority of aneuploid embryos were simple aneuploid, i.e., one or two whole-chromosome imbalances. Structural chromosome aberrations, which are common in cleavage stage embryos, occurred in only three blastocysts (5.8%). All TE biopsies derived from the same embryos were concordant. Forty-nine of fifty-one (96.1%) inner cell mass (ICM) samples were concordant with TE biopsies derived from the same embryos. Discordance between TE and ICM occurred only in the two embryos with structural chromosome aberration. We conclude that trophectoderm karyotype is an excellent predictor of inner cell mass karyotype. Discordance between TE and ICM occurred only in embryos with structural chromosome aberrations.
2010-09-28 | GSE22864 | GEO
Project description:Expt 6---Comprative transcriptomics of euploid and aneuploid Candida albicans strains
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Project description:Aneuploidy, a condition characterized by whole chromosome gains and losses, is often associated with significant cellular stress and decreased fitness. However, whether and how cells respond to the aneuploid state has remained controversial. In aneuploid budding yeast, two opposing gene expression patterns have been reported: an environmental stress response (ESR) and a “common aneuploidy gene-expression” (CAGE) signature, in which many ESR genes are oppositely regulated. Here, we investigate and bring clarity to this controversy. We show that the CAGE signature is not an aneuploidy-specific gene expression signature but is the result of euploid control cells, but not aneuploid cells, having grown into stationary phase. Because growth into stationary phase is amongst the strongest inducers of the ESR, the ESR in aneuploid cells was masked when stationary phase euploid cells were used for normalization in transcriptomic studies. When exponentially growing euploid cells are used in gene expression comparisons with aneuploid cells, the CAGE signature is no longer evident in aneuploid cells. Instead, aneuploid cells are found to exhibit the ESR. We further show that the ESR causes a selective loss of ribosomes in aneuploid cells, providing an explanation for the decreased cellular density in aneuploid cells. We conclude that aneuploid budding yeast cells mount the ESR, rather than a CAGE signature, in response to aneuploidy-induced cellular stresses that results in selective ribosome loss.
2020-06-16 | GSE146791 | GEO
Project description:Study question: Could extracellular vesicles (EVs) secreted by aneuploid embryos a) serve for development of RNA biomarkers for preimplantation genetic testing for aneuploidy (PGT-A) and b) elicit a relevant transcriptomic response in decidualised primary endometrial stromal cells (dESCs)? Summary answer: Aneuploid embryo EVs a) contain genes PPM1J, LINC00561, ANKRD34C and TMED10 in differential abundance from euploid EVs and b) induce up-regulation of MUC1 transcript in dESCs. What is known already: PGT-A is popular as it is thought to facilitate transfer of euploid embryos to increase implantation probability but the technology is controversial, as it requires an invasive embryo biopsy with an elusive long-term biosafety. The development of non-invasive methods to screen out aneuploid embryos is paramount. It is also critical to decode the embryo-endometrial dialog underlying implantation failure. We have previously reported that IVF embryos secrete EVs that can be internalised by ESCs, conceptualising that successful implantation to the endometrium is facilitated by EVs, which may additionally serve as biomarkers of ploidy status. Study design, size, duration: Embryos destined for biopsy on days 5-7 for PGT-A were grown under standard conditions. Spent media (30μl) were collected from euploid (n=175) and aneuploid (n=140)embryos at cleavage (days 1-3) stage and from euploid (n=187) and aneuploid (n=142) embryos at blastocyst (days 3-5) stage. Media samples from n=35 cleavage embryos were pooled in order to obtain five euploid and four aneuploid pools. Similarly, media samples from blastocyst were pooled to create one euploid and one aneuploid pool. ESCs were obtained from five women undergoing diagnostic laparoscopy. Participants/materials, setting, methods: EVs were isolated from pools of media derived from euploid and aneuploid day 3 embryos with differential centrifugation and EV-RNA sequencing was performed following the SMARTer Stranded Total RNA-Seq approach. ESCs were decidualised (E2:10nM, P4:1uM, cAMP:0.5 mM twice every 48 hours) and treated for 24 hours with 50 ng/ml euploid or aneuploid EVs extracted from blastocyst media. RNA sequencing was performed on ESCs following the Illumina Truseq RNAseq protocol. Main results and the role of chance: Aneuploid cleavage stage embryos secreted EVs that were less abundant in RNA fragments originating from the genes PPM1J (log2fc=-5.13, p=0.011), LINC00561 (log2fc=-7.87, p=0.010) and ANKRD34C (log2fc=-7.30, p=0.017) and more abundant in TMED10 (log2fc=1.63 p=0.025) compared to EVs from euploid embryos. Decidualisation per se induced downregulation of MUC1 (log2FC=-0.54, p=0.0028) in ESCs as prerequisite for the establishment of receptive endometrium. The expression of MUC1 transcript in decidualised ESCs was significantly increased following treatment with aneuploid compared to euploid embryo-secreted EVs (log2FC=0.85, p=0.0201). Limitations, reasons for caution: The findings of the study may require validation utilising a second cohort of EVs samples. Wider implications of the findings: The discovery that the RNA cargo of EVs secreted from aneuploid cleavage stage embryos is diverse from that of euploid embryos potentiates the development of non-invasive methodology for PGT-A. The upregulation of MUC1 in dESCs following aneuploid embryo EV treatment proposes a new mechanism underlying implantation failure. Funding: The study was supported by a MSCA fellowship awarded to SM by the European Commission (CERVINO grant agreement ID: 79620) and by a BIRTH research grant from Theramex HQ UK Ltd
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