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Total Stranded paired end RNA Seq of wildtype and knockout Kdm4a 2 cell embryos

ABSTRACT: Total Stranded paired end RNA Seq of wildtype and knockout Kdm4a 2 cell embryos

PROVIDER: PRJNA532606 | ENA |

REPOSITORIES: ENA

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Total Stranded paired end RNA Seq of wildtype and knockout Kdm4a 2 cell embryos

Project description:Purpose: The goal of this study was to generate paired-end total RNA Seq transcriptomes of wildtype and Kdm4a 2 cell embryos to study the dynamics of differentially expressed repeats and transposons during early murine development Methods: 2 cell embryos cultured in KSOM EmbryoMax medium (Sigma) were subjected to the SMARTSeq Stranded Total RNASeq protocol according to the manufacturers instructions on the same day simultaneously for control and knockout embryos. Conclusions: Our study represents a detailed analysis of differentially expressed repeats and transposons in embryos lacking maternal or endogenous Kdm4a, with six biologic replicates, generated by SMARTSeq STranded paired end RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that there is a consistent downrgulation of specific LTR families afffected in most biological replicates, by the lack of Kdm4a giving us robust statistical significance. We conclude that Kdm4a is required for proper activation of these repeat elements in conjuction with a permissive chromatin landscape.

2020-01-30 | GSE129733 | GEO

SMARTSeq_v4 paired end mRNA Seq of Kdm4a control mutant oocytes and preimplantation embryos

Project description:Purpose: The goal of this study was to generate paired-end mRNA Seq transcriptomes of control and Kdm4a mutant oocytes, 2-cell, 4-cell and 8-cell preimplantation embryos to study the dynamics of differentially expressed genes during early development Methods: MII oocytes were isolated from wildtype and Kdm4a knockout mice. 16 MII oocytes from each genotype were washed in M2 medim after zona pellucida removal, washed once in nuclease free water and directly lysed and cDNA prepared according to the manufacturers instructions. Meanwhile, control and knockout MII oocytes were also in vitro fertilised with Kdm4a knockout sperm to produce control (+/-) and maternal mutant (-/-) embryos, and cultured in KSOM EmbryoMax medium (Sigma). 16 embryos were staged each day and harvested according to control embryos. Healthiest mutants were chosen for comparison with minimal secondary effects arising from dead/dying embryos. Similar to oocytes, individual cDNA were prepared and amplified according to manufacturers instructions in nuclease free conditions. Conclusions: Our study represents a detailed analysis of differentially expressed genes in oocytes and embryos lacking maternal and endogenous Kdm4a, with sixteen biological replicates, generated by SMARTSeq v4 paired end RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles between the samples at each developmental stage. Our results show that there is a consistent downrgulation of zygotic genome activation (ZGA) genes in the mutant 2-cell embryos. Mutant 4 and 8-cell embryos have significant upregulation of minor ZGA genes giving us robust statistical significance. We conclude that Kdm4a is required for proper gene activation during maternal-to zygotic transition in conjuction with a permissive chromatin landscape.

2020-01-30 | GSE129731 | GEO

Differentially expressed genes from RNA-Seq and functional enrichment results are affected by the choice of single-end versus paired-end reads and stranded versus non-stranded protocols

Project description:We undertook four mammalian transcriptomics experiments to compare the effect of read mapping, feature counting and differential expression analysis using single-end (SE) and paired-end (PE) protocols. For three of these experiments we also compared a non-stranded (NS) and a strand-specific approach to mapping the paired-end data.

2017-06-09 | GSE97471 | GEO

SMARTSeq_v4 paired end mRNA Seq of Kdm4a control mutant oocytes and preimplantation embryos

Project description:SMARTSeq_v4 paired end mRNA Seq of Kdm4a control mutant oocytes and preimplantation embryos

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Paired end protocol test

Project description:Paired end protocol test

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Differentially expressed genes from RNA-Seq and functional enrichment results are affected by the choice of single-end versus paired-end reads and stranded versus non-stranded protocols

Project description:Differentially expressed genes from RNA-Seq and functional enrichment results are affected by the choice of single-end versus paired-end reads and stranded versus non-stranded protocols

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Zebrafish Paired End DiTag libraries

Project description:Used a DNA tag sequencing and mapping strategy called gene identification signature (GIS) analysis, in which 5' and 3' signatures of full-length cDNAs are accurately extracted into paired-end ditags (PETs) that are concatenated for efficient sequencing and mapped to genome sequences to demarcate the transcription boundaries of every gene. GIS analysis is potentially 30-fold more efficient than standard cDNA sequencing approaches for transcriptome characterization. Keywords: Paired End DiTags

2008-12-01 | GSE6694 | GEO

Paired-end RNA-seq in HepG2 cells

Project description:Paired-end RNA-seq in HepG2 cells

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2.5 dpc female HPG axis RNASeq of Kdm4a wildtype and knockout mice

Project description:Purpose: We performed RNA-Seq on 2.5dpc mouse hypothalamus, pituitary, ovary and uterus of 8-10 week old littermate female control and Kdm4a knockout mice. Upon observing for the extent of altered genes of physiological relevance to observed female infertility phenotype, this would help us narrow down the most relevant tissue to perform genome wide ChipSeq binding profiles for Kdm4a, H3K4me3 and H3K9me3. This dataset would present likely target genes under direct control of Kdm4a.

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Zebrafish Paired End DiTag libraries

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