Genes identified as expressed lower (down) in the AJ strain than in the NOD strain. Differentially expressed genes had a Q-value < 0.05 following the Benjamini-Hochberg methodology for false discovery rates in the limma+voom pipeline within edgeR. Q-value is reported from the topTable function.
Genes identified as expressed lower (down) in the AJ strain than in the CAST strain. Differentially expressed genes had a Q-value < 0.05 following the Benjamini-Hochberg methodology for false discovery rates in the limma+voom pipeline within edgeR. Q-value is reported from the topTable function.
Genes identified as expressed lower (down) in the AJ strain than in the NZO strain. Differentially expressed genes had a Q-value < 0.05 following the Benjamini-Hochberg methodology for false discovery rates in the limma+voom pipeline within edgeR. Q-value is reported from the topTable function.
Genes identified as expressed lower (down) in the AJ strain than in the NOD strain. Differentially expressed genes had a Q-value < 0.05 following the Benjamini-Hochberg methodology for false discovery rates in the limma+voom pipeline within edgeR. Q-value is reported from the topTable function.
Genes identified as expressed lower (down) in the AJ strain than in the PWK strain. Differentially expressed genes had a Q-value < 0.05 following the Benjamini-Hochberg methodology for false discovery rates in the limma+voom pipeline within edgeR. Q-value is reported from the topTable function.
Genes identified as expressed lower (down) in the AJ strain than in the NZO strain. Differentially expressed genes had a Q-value < 0.05 following the Benjamini-Hochberg methodology for false discovery rates in the limma+voom pipeline within edgeR. Q-value is reported from the topTable function.
Genes identified as expressed lower (down) in the AJ strain than in the WSB strain. Differentially expressed genes had a Q-value < 0.05 following the Benjamini-Hochberg methodology for false discovery rates in the limma+voom pipeline within edgeR. Q-value is reported from the topTable function.
Genes identified as expressed lower (down) in the AJ strain than in the CAST strain. Differentially expressed genes had a Q-value < 0.05 following the Benjamini-Hochberg methodology for false discovery rates in the limma+voom pipeline within edgeR. Q-value is reported from the topTable function.
Genes identified as expressed higher (up) in the AJ strain than in the AJ strain. Differentially expressed genes had a Q-value < 0.05 following the Benjamini-Hochberg methodology for false discovery rates in the limma+voom pipeline within edgeR. Q-value is reported from the topTable function.
Genes identified as expressed lower (down) in the AJ strain than in the NOD strain. Differentially expressed genes had a Q-value < 0.05 following the Benjamini-Hochberg methodology for false discovery rates in the limma+voom pipeline within edgeR. Q-value is reported from the topTable function.
Genes identified as expressed lower (down) in the AJ strain than in the NZO strain. Differentially expressed genes had a Q-value < 0.05 following the Benjamini-Hochberg methodology for false discovery rates in the limma+voom pipeline within edgeR. Q-value is reported from the topTable function.
Genes identified as expressed lower (down) in the AJ strain than in the PWK strain. Differentially expressed genes had a Q-value < 0.05 following the Benjamini-Hochberg methodology for false discovery rates in the limma+voom pipeline within edgeR. Q-value is reported from the topTable function.
Genes identified as expressed lower (down) in the AJ strain than in the WSB strain. Differentially expressed genes had a Q-value < 0.05 following the Benjamini-Hochberg methodology for false discovery rates in the limma+voom pipeline within edgeR. Q-value is reported from the topTable function.
Genes identified as expressed higher (up) in the AJ strain than in the AJ strain. Differentially expressed genes had a Q-value < 0.05 following the Benjamini-Hochberg methodology for false discovery rates in the limma+voom pipeline within edgeR. Q-value is reported from the topTable function.
Genes identified as expressed higher (up) in the AJ strain than in the AJ strain. Differentially expressed genes had a Q-value < 0.05 following the Benjamini-Hochberg methodology for false discovery rates in the limma+voom pipeline within edgeR. Q-value is reported from the topTable function.
Mice exposed to morphine drank about 5mL per animal per day (Fig. 1A). Male and female mice on a C57Bl/6J background were used in all studies. Experiments to manipulate mu-opioid receptor-expressing neurons used MOR-Cre mice developed in our lab. These MOR-Cre mice were then crossed with RosaLSLSun1-sfGFP [29] to generate a reporter line for visualization of MORs or Rosa26LSL-EGFP-L10a [30] for cell-type specific RNA sequencing. Mice were 8–12 weeks at the start of each experiment. Mice were sacrificed between 1200 and 1400h and, for each mouse, a gross dissection targeted at the PVT was used to generate tissue for the translating ribosome affinity purification (TRAP). We used both control mice and mice exposed to chronic morphine for TRAP. Due to the small amount of brain tissue, 2 PVT dissections were pooled together to create each biological sample—males were only pooled with males and females were only pooled with females, for a total of four biological replicates for each of the morphine and control groups. RNA sequencing of the MOR+expressing neurons in the PVT that were affinity purified by Translating Ribosome Affinity Purification (TRAP) and subsequent DE analysis identified 311 upregulated and 211 downregulated genes in the morphine group as compared to the control group (multiple-testing-adjusted P value <0.05).
Authors:
Darrell Eacret, Elisabetta Manduchi, Julia Noreck, Emma Tyner, Polina Fenik, Amelia D Dunn, Jonathan Schug, Sigrid C Veasey, Julie A Blendy
Mice exposed to morphine drank about 5mL per animal per day (Fig. 1A). Male and female mice on a C57Bl/6J background were used in all studies. Experiments to manipulate mu-opioid receptor-expressing neurons used MOR-Cre mice developed in our lab. These MOR-Cre mice were then crossed with RosaLSLSun1-sfGFP [29] to generate a reporter line for visualization of MORs or Rosa26LSL-EGFP-L10a [30] for cell-type specific RNA sequencing. Mice were 8–12 weeks at the start of each experiment. Mice were sacrificed between 1200 and 1400h and, for each mouse, a gross dissection targeted at the PVT was used to generate tissue for the translating ribosome affinity purification (TRAP). We used both control mice and mice exposed to chronic morphine for TRAP. Due to the small amount of brain tissue, 2 PVT dissections were pooled together to create each biological sample—males were only pooled with males and females were only pooled with females, for a total of four biological replicates for each of the morphine and control groups. RNA sequencing of the MOR+expressing neurons in the PVT that were affinity purified by Translating Ribosome Affinity Purification (TRAP) and subsequent DE analysis identified 311 upregulated and 211 downregulated genes in the morphine group as compared to the control group (multiple-testing-adjusted P value <0.05).
Authors:
Darrell Eacret, Elisabetta Manduchi, Julia Noreck, Emma Tyner, Polina Fenik, Amelia D Dunn, Jonathan Schug, Sigrid C Veasey, Julie A Blendy
Perinatal fentanyl exposed DEG in female mouse NAc_pvalue
Description:
We identified individual genes with significant gene expression changes following perinatal fentanyl exposure. Pregnant C57BL/6 dams received 10μg/ml fentanyl in their drinking water from embryonic day 0 (E0) through birth until weaning at postnatal day 21 (P21). Liquid consumption by dams all through gestation to weaning was comparable between water and fentanyl in water group. Post-weaning, at P35, we performed an unbiased transcriptomic analysis in perinatal fentanyl exposed mice using high-throughput RNAseq of bulk-tissue punches from VTA, NAc, PrL, S1 and VBT from four juvenile (P35) mice per sex/treatment. For RNA sequencing, only samples with RNA integrity numbers >8 were used. Samples were sequenced on an Illumina HiSeq 4000 with a 75bp paired-end read. 64–100 million reads were obtained for each sample. Reads were aligned to the mouse genome (Mus musculus. GRCm38) using TopHat2 (version 2.0.8; maximum number of mismatches=2; segment length=30; maximum multi-hits per read=25; maximum intron length=50,000). A False Discovery Rate (FDR)<0.05 was used to define differentially expressed genes.
Authors:
Jimmy Olusakin, Gautam Kumar, Mahashweta Basu, Cali A Calarco, Megan E Fox, Jason B Alipio, Catherine Haga, Makeda D Turner, Asaf Keller, Seth A Ament, Mary Kay Lobo
Perinatal fentanyl exposed DEG in female mouse NAc_qvalue
Description:
We identified individual genes with significant gene expression changes following perinatal fentanyl exposure. Pregnant C57BL/6 dams received 10μg/ml fentanyl in their drinking water from embryonic day 0 (E0) through birth until weaning at postnatal day 21 (P21). Liquid consumption by dams all through gestation to weaning was comparable between water and fentanyl in water group. Post-weaning, at P35, we performed an unbiased transcriptomic analysis in perinatal fentanyl exposed mice using high-throughput RNAseq of bulk-tissue punches from VTA, NAc, PrL, S1 and VBT from four juvenile (P35) mice per sex/treatment. For RNA sequencing, only samples with RNA integrity numbers >8 were used. Samples were sequenced on an Illumina HiSeq 4000 with a 75bp paired-end read. 64–100 million reads were obtained for each sample. Reads were aligned to the mouse genome (Mus musculus. GRCm38) using TopHat2 (version 2.0.8; maximum number of mismatches=2; segment length=30; maximum multi-hits per read=25; maximum intron length=50,000). A False Discovery Rate (FDR)<0.05 was used to define differentially expressed genes.
Authors:
Jimmy Olusakin, Gautam Kumar, Mahashweta Basu, Cali A Calarco, Megan E Fox, Jason B Alipio, Catherine Haga, Makeda D Turner, Asaf Keller, Seth A Ament, Mary Kay Lobo
DEG female mouse forebrain PND1 morphine vs saline_pvalue
Description:
To examine forebrain transcriptomic changes that might elucidate mechanisms of withdrawal, delayed development, and any long-term behavior changes, we generated transcriptomic signatures following our “3-trimester” exposure model (3-Tri). In addition, we also examined transcriptomes from animals that received opioids only during the gestational period (PND1) or only during the last trimester from PND 1–14 (PND 14). We sought to determine whether transcriptomic signatures vary based on the window of exposure, perhaps contributing to the discrepancies in the literature regarding acute and long-term outcomes. Brains were dissected from PND 1 pups 6 h after discovery. Brains were dissected from post-natal exposure only (PND 14) or 3-trimester exposure (3-tri) 6 h after the last morphine or saline injection. The number of animals per group was similar (N = 5–7 animals, male and female C57Bl/6NTac mice), and the quality controls, library construction and sequence parameters were also identical across all groups. Libraries were sequenced on a NovaSeq 6000 at a depth of 30 million total reads/sample using paired-end sequencing of 150 base pairs (PE150), to a depth of 30 million total reads/sample. Reads were then mapped to the mouse reference genome (Mus Musculus, GRCm38/mm10) using HISAT2 (version 2.2.1), and duplicated fragments were removed using Picard MarkDuplicates. Differential expression analysis between two conditions (e.g., Morphine and Saline) was performed in R (version 4.1.1) with DESeq2 (v1.32.0) package. Genes were assigned by the authors as differentially expressed if the (adjusted) (nominal) p-value < 0.05. All genes/scores are presented here.
Authors:
Amelia D Dunn, Shivon A Robinson, Chiso Nwokafor, Molly Estill, Julia Ferrante, Li Shen, Crystal O Lemchi, Jordi Creus-Muncunill, Angie Ramirez, Juliet Mengaziol, Julia K Brynildsen, Mark Leggas, Jamie Horn, Michelle E Ehrlich, Julie A Blendy
DEG male mouse forebrain 3-tri morphine vs saline_pvalue
Description:
To examine forebrain transcriptomic changes that might elucidate mechanisms of withdrawal, delayed development, and any long-term behavior changes, we generated transcriptomic signatures following our “3-trimester” exposure model (3-Tri). In addition, we also examined transcriptomes from animals that received opioids only during the gestational period (PND1) or only during the last trimester from PND 1–14 (PND 14). We sought to determine whether transcriptomic signatures vary based on the window of exposure, perhaps contributing to the discrepancies in the literature regarding acute and long-term outcomes. Brains were dissected from PND 1 pups 6 h after discovery. Brains were dissected from post-natal exposure only (PND 14) or 3-trimester exposure (3-tri) 6 h after the last morphine or saline injection. The number of animals per group was similar (N = 5–7 animals, male and female C57Bl/6NTac mice), and the quality controls, library construction and sequence parameters were also identical across all groups. Libraries were sequenced on a NovaSeq 6000 at a depth of 30 million total reads/sample using paired-end sequencing of 150 base pairs (PE150), to a depth of 30 million total reads/sample. Reads were then mapped to the mouse reference genome (Mus Musculus, GRCm38/mm10) using HISAT2 (version 2.2.1), and duplicated fragments were removed using Picard MarkDuplicates. Differential expression analysis between two conditions (e.g., Morphine and Saline) was performed in R (version 4.1.1) with DESeq2 (v1.32.0) package. Genes were assigned by the authors as differentially expressed if the (adjusted) (nominal) p-value < 0.05. All genes/scores are presented here.
Authors:
Amelia D Dunn, Shivon A Robinson, Chiso Nwokafor, Molly Estill, Julia Ferrante, Li Shen, Crystal O Lemchi, Jordi Creus-Muncunill, Angie Ramirez, Juliet Mengaziol, Julia K Brynildsen, Mark Leggas, Jamie Horn, Michelle E Ehrlich, Julie A Blendy
DEG female mouse forebrain PND14 morphine vs saline_pvalue
Description:
To examine forebrain transcriptomic changes that might elucidate mechanisms of withdrawal, delayed development, and any long-term behavior changes, we generated transcriptomic signatures following our “3-trimester” exposure model (3-Tri). In addition, we also examined transcriptomes from animals that received opioids only during the gestational period (PND1) or only during the last trimester from PND 1–14 (PND 14). We sought to determine whether transcriptomic signatures vary based on the window of exposure, perhaps contributing to the discrepancies in the literature regarding acute and long-term outcomes. Brains were dissected from PND 1 pups 6 h after discovery. Brains were dissected from post-natal exposure only (PND 14) or 3-trimester exposure (3-tri) 6 h after the last morphine or saline injection. The number of animals per group was similar (N = 5–7 animals, male and female C57Bl/6NTac mice), and the quality controls, library construction and sequence parameters were also identical across all groups. Libraries were sequenced on a NovaSeq 6000 at a depth of 30 million total reads/sample using paired-end sequencing of 150 base pairs (PE150), to a depth of 30 million total reads/sample. Reads were then mapped to the mouse reference genome (Mus Musculus, GRCm38/mm10) using HISAT2 (version 2.2.1), and duplicated fragments were removed using Picard MarkDuplicates. Differential expression analysis between two conditions (e.g., Morphine and Saline) was performed in R (version 4.1.1) with DESeq2 (v1.32.0) package. Genes were assigned by the authors as differentially expressed if the (adjusted) (nominal) p-value < 0.05. All genes/scores are presented here.
Authors:
Amelia D Dunn, Shivon A Robinson, Chiso Nwokafor, Molly Estill, Julia Ferrante, Li Shen, Crystal O Lemchi, Jordi Creus-Muncunill, Angie Ramirez, Juliet Mengaziol, Julia K Brynildsen, Mark Leggas, Jamie Horn, Michelle E Ehrlich, Julie A Blendy
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