The parts of a GENOME sequence that are involved with the different functions or properties of genomes as a whole as opposed to those of individual GENES.
Generated by gene2mesh v. 1.1.1
The genetic complement of an organism, including all of its GENES, as represented in its DNA, or in some cases, its RNA.
Generated by gene2mesh v. 1.1.1
The processes, properties and biological objects that are involved in maintaining, expressing, and transmitting from one organism to another, genetically encoded traits.
Generated by gene2mesh v. 1.1.1
The biological objects that contain genetic information and that are involved in transmitting genetically encoded traits from one organism to another.
Generated by gene2mesh v. 1.1.1
Postmortem human brain tissue from the caudate nucleus region of a total of 48 individuals with Alcohol Use Disorder (AUD) and 51 control individuals were taken and RNA extracted from frozen tissue. Sequencing was carried out using the NovaSeq 6000 (Illumina) platform, and gene expression analysis was carried out with respect to AUD and control samples. Gene symbols from Entrez ids are used and Logbase2 FC as provided by the authors are annotated.
Authors:
Lea Zillich, Eric Poisel, Josef Frank, Jerome C Foo, Marion M Friske, Fabian Streit, Lea Sirignano, Stefanie Heilmann-Heimbach, André Heimbach, Per Hoffmann, Franziska Degenhardt, Anita C Hansson, Georgy Bakalkin, Markus M Nöthen, Marcella Rietschel, Rainer Spanagel, Stephanie H Witt
Postmortem human brain tissue from the putamen region of a total of 48 individuals with Alcohol Use Disorder (AUD) and 51 control individuals were taken and RNA extracted from frozen tissue. Sequencing was carried out using the NovaSeq 6000 (Illumina) platform, and gene expression analysis was carried out with respect to AUD and control samples. Gene symbols from Entrez ids are used and Logbase2 FC as provided by the authors are annotated.
Authors:
Lea Zillich, Eric Poisel, Josef Frank, Jerome C Foo, Marion M Friske, Fabian Streit, Lea Sirignano, Stefanie Heilmann-Heimbach, André Heimbach, Per Hoffmann, Franziska Degenhardt, Anita C Hansson, Georgy Bakalkin, Markus M Nöthen, Marcella Rietschel, Rainer Spanagel, Stephanie H Witt
Postmortem human brain tissue from the ventral striatum from postmortem human brain tissue with Alcohol Use Disorder (AUD) region of a total of 48 individuals with Alcohol Use Disorder (AUD) and 51 control individuals were taken and RNA extracted from frozen tissue. Sequencing was carried out using the NovaSeq 6000 (Illumina) platform, and gene expression analysis was carried out with respect to AUD and control samples. Gene symbols from Entrez ids are used and Logbase2 FC as provided by the authors are annotated.
Authors:
Lea Zillich, Eric Poisel, Josef Frank, Jerome C Foo, Marion M Friske, Fabian Streit, Lea Sirignano, Stefanie Heilmann-Heimbach, André Heimbach, Per Hoffmann, Franziska Degenhardt, Anita C Hansson, Georgy Bakalkin, Markus M Nöthen, Marcella Rietschel, Rainer Spanagel, Stephanie H Witt
Dysregulation of NRSF/REST via EHMT1 is associated with psychiatric disorders and Kleefstra syndrome, Z scores
Description:
EHMT1 is an epigenetic repressor that is causal for Kleefstra Syndrome (KS), a neurodevelopmental disorder (NDD) leading to intelectual disability, and is associated with schizophrenia. Here, the researchers aim to show we show that reduced EHMT1 activity decreases NRSF/REST protein leading to abnormal neuronal gene expression and progression of neurodevelopment in human iPSC. Five induced pluripotent stem cell samples (from fibroblasts of adult, male, skin) were used. The stem cells were gifted from: Lieber Institute for Brain Development, Johns Hopkins Medical Campus. Total RNA extracted from a control hiPSC line and control cells treated for 72h with various concentrations of UNC0638 i.e 50, 100, 200 or 250nM as a model for Kleefstra syndrome. Polyadenylated adaptors were ligated to the 3′-end, 5′-adaptors were then ligated, and the resulting RNAs were reverse transcribed to generate cDNA that can be amplified by PCR. The amplified product was run on low range ultra agarose in TBE buffer and a size-selection was performed to ensure that the cDNA used for sequencing primarily contains miRNAs rather than other RNA contaminants. Expression values were calculated by the method detailed in 'HBA-DEALS: accurate and simultaneous identification of differential expression and splicing using hierarchical Bayesian analysis' (Genome Biol. 2020, PMID: 32660516), and Z scores calculated. Genes were annotated as Ensembl gene ids. SRA Study id ERP130338.
Differentially expressed genes from RPE compared to Normal Retina
Description:
Transcriptome profiling from macular retina and RPE/choroid samples from 27 unrelated eye tissue donors, was performed using RNA-sequencing. Human donor eye collection were obtained from Utah Lions Eye Bank within a 6-hour post-mortem interval and donors aged 60-90 years. Sample types were Normal Retina, Intermediate AMD Retina, Neovascular AMD Retina, Normal macular retina pigment epithelium (RPE), Intermediate AMD RPE, and Neovascular AMD RPE. Age Related Macular Degeneration (AMD) phenotyping was determined using the Age-Related Eye Disease Study (AREDS) severity grading scale, where AREDS category 0/1 was considered normal, AREDS category 3 intermediate AMD, and AREDS category 4b neovascular AMD. Samples from Normal RPE were compared to Normal Retina, and are presented with fold change > 1.5 and and P < 0.05. This gene set was annotated from the Supplementry Table of BioRxiv pre-print paper ‘Patterns of gene expression and allele-specific expression vary among macular tissues and clinical stages of Age-related Macular Degeneration’ by Zhang et.al (2022) doi: https://doi.org/10.1101/2022.12.19.521092
RNA sequencing of a limited number of archived patients' specimens with extended opioid exposure or non-opioid exposure was performed. Immune infiltration and changes in the microenvironment were evaluated using CIBERSORT.
Authors:
Mamatha Garige, Sarah Poncet, Alexis Norris, Chao-Kai Chou, Wells W Wu, Rong-Fong Shen, Jacob W Greenberg, Louis Spencer Krane, Carole Sourbier
The dataset used in this study (Bulk RNA-Seq) was previously published and can be found at NCBI GEO (GSE182321), this analysis was conducted by GEO2R to compare control and OUD samples, only top differentially expressed genes are reported. To understand mechanisms and identify potential targets for intervention in the current crisis of opioid use disorder (OUD), postmortem brains represent an under-utilized resource. To refine previously reported gene signatures of neurobiological alterations in OUD from the dorsolateral prefrontal cortex (Brodmann Area 9, BA9), we explored the role of microRNAs (miRNA) as powerful epigenetic regulators of gene function.
The dataset used in this study (Bulk RNA-Seq) was previously published and can be found at NCBI GEO (GSE182321), this analysis was conducted by GEO2R to compare control and OUD samples, only top differentially expressed genes are reported. To understand mechanisms and identify potential targets for intervention in the current crisis of opioid use disorder (OUD), postmortem brains represent an under-utilized resource. To refine previously reported gene signatures of neurobiological alterations in OUD from the dorsolateral prefrontal cortex (Brodmann Area 9, BA9), we explored the role of microRNAs (miRNA) as powerful epigenetic regulators of gene function.
Transcriptional alterations in dorsolateral prefrontal cortex and nucleus accumbens implicate neuroinflammation and synaptic remodeling in opioid use disorder. Transcriptomic profile of 20 control subjects and 20 OUD subjects in brain region DLPFC and NAC. Analyzed using GEO2R (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE174409) separately for each brain region, comparing OUD and control samples.
Authors:
Xiangning Xue, Wei Zong, Jill R Glausier, Sam-Moon Kim, Micah A Shelton, BaDoi N Phan, Chaitanya Srinivasan, Andreas R Pfenning, George C Tseng, David A Lewis, Marianne L Seney, Ryan W Logan
Transcriptional alterations in dorsolateral prefrontal cortex and nucleus accumbens implicate neuroinflammation and synaptic remodeling in opioid use disorder. Transcriptomic profile of 20 control subjects and 20 OUD subjects in brain region DLPFC and NAC. Analyzed using GEO2R (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE174409) separately for each brain region, comparing OUD and control samples.
Authors:
Xiangning Xue, Wei Zong, Jill R Glausier, Sam-Moon Kim, Micah A Shelton, BaDoi N Phan, Chaitanya Srinivasan, Andreas R Pfenning, George C Tseng, David A Lewis, Marianne L Seney, Ryan W Logan
Differential gene expression between CS15 and CS22 - Log2FC
Description:
Human craniofacial tissues were collected from the Joint MRC/Wellcome Trust Human Developmental Biology (HDBR). Donations of tissue to HDBR are made under-informed ethical consent with Research Tissue Bank ethical approval by women undergoing termination of pregnancy. Gene expression profiles were generated from multiple biological replicates of primary craniofacial (CF) tissue from Carnegie Stages (CS) of the embryonic period, CS13, CS14, CS17, CS17, and CS22. Here the differential expression comparison between CS15 and CS22 is shown. Gene expressions values with log to the base 2, FC are presented with P-Adj <0.05. UBERON:0015789, cranial or facial muscle.
Authors:
Tara N Yankee, Sungryong Oh, Emma Wentworth Winchester, Andrea Wilderman, Kelsey Robinson, Tia Gordon, Jill A Rosenfeld, Jennifer VanOudenhove, Daryl A Scott, Elizabeth J Leslie, Justin Cotney
Differential gene expression between CS15 and CS22 - Adj-P value
Description:
Human craniofacial tissues were collected from the Joint MRC/Wellcome Trust Human Developmental Biology (HDBR). Donations of tissue to HDBR are made under-informed ethical consent with Research Tissue Bank ethical approval by women undergoing termination of pregnancy. Gene expression profiles were generated from multiple biological replicates of primary craniofacial (CF) tissue from Carnegie Stages (CS) of the embryonic period, CS13, CS14, CS17, CS17 and CS22. Here the differential expression comparison between CS15 and CS22 is shown. Gene expressions values, Ensembl Gene ids and the corresponding Adjusted P value are presented. UBERON:0015789, cranial or facial muscle.
Authors:
Tara N Yankee, Sungryong Oh, Emma Wentworth Winchester, Andrea Wilderman, Kelsey Robinson, Tia Gordon, Jill A Rosenfeld, Jennifer VanOudenhove, Daryl A Scott, Elizabeth J Leslie, Justin Cotney
Differential gene expression between CS13 and CS22 - Log2FC
Description:
Human craniofacial tissues were collected from the Joint MRC/Wellcome Trust Human Developmental Biology (HDBR). Donations of tissue to HDBR are made under-informed ethical consent with Research Tissue Bank ethical approval by women undergoing termination of pregnancy. Gene expression profiles were generated from multiple biological replicates of primary craniofacial (CF) tissue from Carnegie Stages (CS) of the embryonic period, CS13, CS14, CS17, CS17, and CS22. Here the differential expression comparison between CS13 and CS22 is shown. Gene expressions values with log to the base 2, FC are presented with P-Adj <0.05. UBERON:0015789, cranial or facial muscle.
Authors:
Tara N Yankee, Sungryong Oh, Emma Wentworth Winchester, Andrea Wilderman, Kelsey Robinson, Tia Gordon, Jill A Rosenfeld, Jennifer VanOudenhove, Daryl A Scott, Elizabeth J Leslie, Justin Cotney
Differential gene expression between CS13 and CS22 - Adj-P value
Description:
Human craniofacial tissues were collected from the Joint MRC/Wellcome Trust Human Developmental Biology (HDBR). Donations of tissue to HDBR are made under-informed ethical consent with Research Tissue Bank ethical approval by women undergoing termination of pregnancy. Gene expression profiles were generated from multiple biological replicates of primary craniofacial (CF) tissue from Carnegie Stages (CS) of the embryonic period, CS13, CS14, CS17, CS17 and CS22. Here the differential expression comparison between CS13 and CS22 is shown. Gene expressions values, Ensembl Gene ids and the corresponding Adjusted P value are presented. UBERON:0015789, cranial or facial muscle.
Authors:
Tara N Yankee, Sungryong Oh, Emma Wentworth Winchester, Andrea Wilderman, Kelsey Robinson, Tia Gordon, Jill A Rosenfeld, Jennifer VanOudenhove, Daryl A Scott, Elizabeth J Leslie, Justin Cotney
Differential gene expression between CS17 and CS22 - Log2FC
Description:
Human craniofacial tissues were collected from the Joint MRC/Wellcome Trust Human Developmental Biology (HDBR). Donations of tissue to HDBR are made under-informed ethical consent with Research Tissue Bank ethical approval by women undergoing termination of pregnancy. Gene expression profiles were generated from multiple biological replicates of primary craniofacial (CF) tissue from Carnegie Stages (CS) of the embryonic period, CS13, CS14, CS17, CS17, and CS22. Here the differential expression comparison between CS17 and CS22 is shown. Gene expressions values with log to the base 2, FC are presented with P-Adj <0.05. UBERON:0015789, cranial or facial muscle.
Authors:
Tara N Yankee, Sungryong Oh, Emma Wentworth Winchester, Andrea Wilderman, Kelsey Robinson, Tia Gordon, Jill A Rosenfeld, Jennifer VanOudenhove, Daryl A Scott, Elizabeth J Leslie, Justin Cotney
Differential gene expression between CS14 and CS22 - Adj-P value
Description:
Human craniofacial tissues were collected from the Joint MRC/Wellcome Trust Human Developmental Biology (HDBR). Donations of tissue to HDBR are made under-informed ethical consent with Research Tissue Bank ethical approval by women undergoing termination of pregnancy. Gene expression profiles were generated from multiple biological replicates of primary craniofacial (CF) tissue from Carnegie Stages (CS) of the embryonic period, CS13, CS14, CS17, CS17 and CS22. Here the differential expression comparison between CS14 and CS22 is shown. Gene expressions values, Ensembl Gene ids and the corresponding Adjusted P value are presented. UBERON:0015789, cranial or facial muscle.
Authors:
Tara N Yankee, Sungryong Oh, Emma Wentworth Winchester, Andrea Wilderman, Kelsey Robinson, Tia Gordon, Jill A Rosenfeld, Jennifer VanOudenhove, Daryl A Scott, Elizabeth J Leslie, Justin Cotney
Differential gene expression between CS14 and CS22 - Log2FC
Description:
Human craniofacial tissues were collected from the Joint MRC/Wellcome Trust Human Developmental Biology (HDBR). Donations of tissue to HDBR are made under-informed ethical consent with Research Tissue Bank ethical approval by women undergoing termination of pregnancy. Gene expression profiles were generated from multiple biological replicates of primary craniofacial (CF) tissue from Carnegie Stages (CS) of the embryonic period, CS13, CS14, CS17, CS17, and CS22. Here the differential expression comparison between CS14 and CS22 is shown. Gene expressions values with log to the base 2, FC are presented with P-Adj <0.05. UBERON:0015789, cranial or facial muscle.
Authors:
Tara N Yankee, Sungryong Oh, Emma Wentworth Winchester, Andrea Wilderman, Kelsey Robinson, Tia Gordon, Jill A Rosenfeld, Jennifer VanOudenhove, Daryl A Scott, Elizabeth J Leslie, Justin Cotney
Differential gene expression between CS14 and CS22 - Adj-P value
Description:
Human craniofacial tissues were collected from the Joint MRC/Wellcome Trust Human Developmental Biology (HDBR). Donations of tissue to HDBR are made under-informed ethical consent with Research Tissue Bank ethical approval by women undergoing termination of pregnancy. Gene expression profiles were generated from multiple biological replicates of primary craniofacial (CF) tissue from Carnegie Stages (CS) of the embryonic period, CS13, CS14, CS17, CS17 and CS22. Here the differential expression comparison between CS14 and CS22 is shown. Gene expressions values, Ensembl Gene ids and the corresponding Adjusted P value are presented. UBERON:0015789, cranial or facial muscle.
Authors:
Tara N Yankee, Sungryong Oh, Emma Wentworth Winchester, Andrea Wilderman, Kelsey Robinson, Tia Gordon, Jill A Rosenfeld, Jennifer VanOudenhove, Daryl A Scott, Elizabeth J Leslie, Justin Cotney
We performed single-nuclei multiome profiling on postmortem caudate nucleus (CN) tissue from six individuals with cocaine use disorder (CocUD) and eight controls, all of African American ancestry. CocUD cases and controls were balanced according to age and sex. We performed single-nuclei ATAC-seq and RNA-seq using the 10x Genomics Multiome platform. Weighted nearest neighbor analysis resulted in an integrated UMAP depicting 13 clearly delineated cell types, including astrocytes, microglia, oligodendrocytes, oligodendrocyte precursor cells (OPC), endothelial cells and lymphocytes, as well as different GABAergic neurons, such as D1 and D2 medium spiny neurons (MSNs) and a small population of cholinergic neurons.
Authors:
Lea Zillich, Annasara Artioli, Veronika Pohořalá, Eric Zillich, Laura Stertz, Hanna Belschner, Ammar Jabali, Josef Frank, Fabian Streit, Diana Avetyan, Maja Völker, Svenja Müller, Anita Hansson, Thomas Meyer, Marcella Rietschel, Rainer Spanagel, Ana Oliveira, Consuelo Walss-Bass, Rick Bernardi, Philipp Koch, Stephanie Witt
DEG human CN astrocytes CocUD vs control_avg log2FC
Description:
We performed single-nuclei multiome profiling on postmortem caudate nucleus (CN) tissue from six individuals with cocaine use disorder (CocUD) and eight controls, all of African American ancestry. CocUD cases and controls were balanced according to age and sex. We performed single-nuclei ATAC-seq and RNA-seq using the 10x Genomics Multiome platform. Weighted nearest neighbor analysis resulted in an integrated UMAP depicting 13 clearly delineated cell types, including astrocytes, microglia, oligodendrocytes, oligodendrocyte precursor cells (OPC), endothelial cells and lymphocytes, as well as different GABAergic neurons, such as D1 and D2 medium spiny neurons (MSNs) and a small population of cholinergic neurons.
Authors:
Lea Zillich, Annasara Artioli, Veronika Pohořalá, Eric Zillich, Laura Stertz, Hanna Belschner, Ammar Jabali, Josef Frank, Fabian Streit, Diana Avetyan, Maja Völker, Svenja Müller, Anita Hansson, Thomas Meyer, Marcella Rietschel, Rainer Spanagel, Ana Oliveira, Consuelo Walss-Bass, Rick Bernardi, Philipp Koch, Stephanie Witt
We performed single-nuclei multiome profiling on postmortem caudate nucleus (CN) tissue from six individuals with cocaine use disorder (CocUD) and eight controls, all of African American ancestry. CocUD cases and controls were balanced according to age and sex. We performed single-nuclei ATAC-seq and RNA-seq using the 10x Genomics Multiome platform. Weighted nearest neighbor analysis resulted in an integrated UMAP depicting 13 clearly delineated cell types, including astrocytes, microglia, oligodendrocytes, oligodendrocyte precursor cells (OPC), endothelial cells and lymphocytes, as well as different GABAergic neurons, such as D1 and D2 medium spiny neurons (MSNs) and a small population of cholinergic neurons.
Authors:
Lea Zillich, Annasara Artioli, Veronika Pohořalá, Eric Zillich, Laura Stertz, Hanna Belschner, Ammar Jabali, Josef Frank, Fabian Streit, Diana Avetyan, Maja Völker, Svenja Müller, Anita Hansson, Thomas Meyer, Marcella Rietschel, Rainer Spanagel, Ana Oliveira, Consuelo Walss-Bass, Rick Bernardi, Philipp Koch, Stephanie Witt
GeneWeaver