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Single-cell analysis of allelic gene expression in pluripotency, differentiation and X-chromosome inactivation

ABSTRACT: We sequenced the mRNAs of embryonic stem cells (ESCs) cultured in different conditions. The two lines M (male) and F (female) used in this study were derived from E4 blastocysts of the same cross between a C57BL/6J (Mus musculus domesticus) and CAST/EiJ (Mus castaneus) male. mESCs were cultured in 2i and LIF as the ground state condition or in serum and LIF as the conventional condition. Epistem cell lines were also generated from the two lines by culturing them with Activin A and FGF2. In order to study more advanced development, we differentiated the two mESC lines through embryonic body formation to postmitotic motor neurons using retinoic acid and the smoothened agonist SAG. This differentiation process also results in the derivation of several types of interneurons. We picked single cells from all different conditions and generated sequencing libraries using the Smart-seq2 and Tn5 protocol. For simplicity, we designate the different condition as ES2i, ES, Epi and Neuron from hereon. We also obtained preimplantation inner cell mass and epiblast cells from E3.5 ICM (inner cell mass) and E4.5 blastocysts of the crossbred mice (male CAST/EiJ × female C57BL/6J) as well as postimplantation epiblast cells from E5.5 embryos of C57BL/6J mice

ORGANISM(S): Mus musculus

PROVIDER: GSE74155 | GEO | 2016/07/27

SECONDARY ACCESSION(S): PRJNA299180

REPOSITORIES: GEO

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Single-cell analysis of allelic gene expression in pluripotency, differentiation and X-chromosome inactivation

Project description:We sequenced the mRNAs of embryonic stem cells (ESCs) cultured in different conditions. The two lines M (male) and F (female) used in this study were derived from E4 blastocysts of the same cross between a C57BL/6J (Mus musculus domesticus) and CAST/EiJ (Mus castaneus) male. mESCs were cultured in 2i and LIF as the ground state condition or in serum and LIF as the conventional condition. Epistem cell lines were also generated from the two lines by culturing them with Activin A and FGF2. In order to study more advanced development, we differentiated the two mESC lines through embryonic body formation to postmitotic motor neurons using retinoic acid and the smoothened agonist SAG. This differentiation process also results in the derivation of several types of interneurons. We picked single cells from all different conditions and generated sequencing libraries using the Smart-seq2 and Tn5 protocol. For simplicity, we designate the different condition as ES2i, ES, Epi and Neuron from hereon. We also obtained preimplantation inner cell mass and epiblast cells from E3.5 ICM (inner cell mass) and E4.5 blastocysts of the crossbred mice (male CAST/EiJ Ã female C57BL/6J) as well as postimplantation epiblast cells from E5.5 embryos of C57BL/6J mice Examination of gene expression profile in individual male and female embryonic stem cell lines along developmental progression

2016-07-27 | E-GEOD-74155 | biostudies-arrayexpress

Compensatory cis-trans regulation of mouse liver gene expression

Project description:Two inbred mouse strains, C57BL/6J and CAST/EiJ, were crossed to generate both initial and reciprocal F1 crosses. For each genetically distinct class of mice (F0 C57BL/6J, F0 CAST/EiJ, F1i - C57BL/6J x CAST/EiJ, F1r - CAST/EiJ x C57BL/6J, where the male parent is listed first), samples were collected from a single lobe of the liver from 6 male mice between the ages of 4 and 6 months. The 24 samples were then processed to generate strand-specific RNA-seq libraries, which were sequenced on the Illumina GAII platform using 72bp paired-end reads.

2012-09-07 | E-MTAB-1091 | biostudies-arrayexpress

RNA-Seq of mESCs based on sex chromosome complement

Project description:RNA-Seq was performed on mESCs generated from F1 hybrids from reciprocal crosses of C57BL/6J and CAST/EiJ, denoted B and C hereafter; cell lines are designated as BC or CB, with the maternal line symbolized first

2017-09-15 | GSE90516 | GEO

Transcriptomic Profiling of Collaborative Cross Founder Mouse Embryonic Fibroblasts stimulated with Type I, II and III Interferons

2014-05-27 | GSE53057 | GEO

Mouse strain-specific chromatin and transcriptional states modulate the DNA-damage response to an inhalational carcinogen

Project description:Genetically distinct individuals are differentially affected by the DNA damaging effects of exposure to environmental toxicants, but the mechanisms contributing to these differences are poorly understood. It is known that genetic variation affects the establishment of the gene regulatory landscape, and we hypothesized that this may significantly contribute to the observed heterogeneity in individual responses to exogenous cellular insults. In this study, we investigated how genetic variation and chromatin organization may dictate susceptibility to DNA damage. We measured DNA damage, mRNA and miRNA expression, and chromatin accessibility genome-wide in lung tissue from two genetically-divergent inbred mouse strains, C57BL/6J and CAST/EiJ, at baseline and in response to exposure to a model DNA-damaging chemical, 1,3-butadiene (BD). Our results show that unexposed CAST/EiJ and unexposed C57BL/6J mice have very different chromatin organization and transcription profiles in the lung. Importantly, in unexposed CAST/EiJ, which is more resistant to BD-induced DNA damage, we see increased transcription and a more accessible chromatin landscape around genes involved in detoxification pathways. Upon BD exposure, chromatin is significantly remodeled in C57BL/6J around these genes to more closely resemble that found in CAST/EiJ. This suggests that strain-specific differences in baseline chromatin organization and transcription contribute to the relative resistance of CAST/EiJ to the DNA damaging effects of BD. Based on these results, we propose more generally that differences in the baseline molecular state of key tissues, driven by unique genetic backgrounds, significantly contributes to inter-individual variability in response to DNA-damaging environmental agents.

2017-08-29 | GSE86623 | GEO

Mus musculus

Project description:CAST/EiJ x C57BL/6J cross data

| PRJNA117247 | ENA

Allelic expression in tibial growth plates from 21 day old C57BL/6J x CAST/EiJ F1s

Project description:We have identified candidate genes from the Feml2 QTL influencing femur length through allele specific expression analysis of growth plates in C57BL/6J x CAST/EiJ F1 hybrids. This work provides the foundation to identify novel genes affecting bone geometry.

2016-11-19 | GSE90055 | GEO

Parent-of-Origin Allelic Expression in the Mouse Cerebellum

Project description:The maternal and paternal genomes play different roles in mammalian brains as a result of genomic imprinting, an epigenetic regulation leading to differential expression of the parental alleles of some genes. Here we investigate genomic imprinting in the cerebellum using a newly developed Bayesian statistical model that provides unprecedented transcript-level resolution. We uncover 160 imprinted transcripts, including 41 novel and independently validated imprinted genes. Strikingly, many genes exhibit parentally biased -rather than monoallelic- expression, with different magnitudes according to age, organ, and brain region. Developmental changes in parental bias and overall gene expression are strongly correlated, suggesting combined roles in regulating gene dosage. These findings reveal the remarkable complexity of genomic imprinting, with important implications for understanding the normal and diseased brain. 48 samples of F1 mouse hybrids produced by crossing C57Bl/6J males with Cast/EiJ females (denoted as F1i) and reciprocally crossing Cast/EiJ males and C57Bl/6J famales (denoted as F1r).

2015-07-07 | E-GEOD-67556 | biostudies-arrayexpress

Transcriptomic Profiling of Collaborative Cross Founder Mouse Embryonic Fibroblasts stimulated with IFN-g and IL28

Project description:Collaborative Cross (CC) mouse embryonic fibroblasts (MEF) cells obtained from the eight Founder animals [PWK/PhJ, NZO/HILtJ, NOD/ShiLtJ, WSB/EiJ, A/J, CAST, C57BL/6J, and 129/SvlmJ] were immortalized and the cell lines used to assess differences in transcriptional responses following treatment with mouse recombinant IFNg and IL28. We collected transcriptome profiles for 8 CC MEF cell lines stimulated with either IFNg or IL28 for a total of 16 different biological conditions. Treated and mock samples were collected at 18 hr post-treatment and RNAs extracted and subjected to microarray.

2016-05-26 | E-MTAB-4690 | biostudies-arrayexpress

Transcriptomic Profiling of Collaborative Cross Founder Mouse Embryonic Fibroblasts stimulated with Type I, II and III Interferons

Project description:Collaborative Cross (CC) mouse embryonic fiborolasts (MEF) cells obtained from the eight Founder animals [PWK/PhJ, NZO/HILtJ, NOD/ShiLtJ, WSB/EiJ, A/J, CAST, C57BL/6J, and 129/SvlmJ] were immortalized and the cell lines used to assess differences in transcriptional responses following treatment with type I, II and III recombinant mouse interferon. We collected transcriptome profiles for 8 CC MEF cell lines stimulated with either IFN-α or IFN-β for a total of 16 different biological conditions. Treated and mock samples were collected at 18 hr post-treatment and RNAs extracted and subjected to microarray.

2014-05-27 | E-GEOD-53057 | biostudies-arrayexpress

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