{"database":"ENA","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Fastqsanger.gz":["ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR639/006/SRR6398796/SRR6398796.fastq.gz","ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR639/005/SRR6398785/SRR6398785.fastq.gz","ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR639/003/SRR6398783/SRR6398783.fastq.gz","ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR639/004/SRR6398794/SRR6398794.fastq.gz","ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR639/002/SRR6398792/SRR6398792.fastq.gz","ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR639/009/SRR6398789/SRR6398789.fastq.gz","ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR639/007/SRR6398787/SRR6398787.fastq.gz","ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR639/000/SRR6398790/SRR6398790.fastq.gz","ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR639/005/SRR6398795/SRR6398795.fastq.gz","ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR639/004/SRR6398784/SRR6398784.fastq.gz","ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR639/007/SRR6398797/SRR6398797.fastq.gz","ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR639/006/SRR6398786/SRR6398786.fastq.gz","ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR639/003/SRR6398793/SRR6398793.fastq.gz","ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR639/002/SRR6398782/SRR6398782.fastq.gz","ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR639/008/SRR6398788/SRR6398788.fastq.gz","ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR639/001/SRR6398791/SRR6398791.fastq.gz"]},"type":"primary"},"statusCodeValue":200,"statusCode":"OK"}],"scores":null,"additional":{"omics_type":["Genomics"],"center_name":["Lund University"],"full_dataset_link":["https://www.ebi.ac.uk/ena/browser/view/PRJNA423285"],"scientific_name":["Mus musculus"],"tag":["xref:PubMed:29581424"],"long_description":["The adult brain is composed of hundreds of different neuronal subtypes, which retain their differentiated traits and identity throughout the lifespan of the organism. Nevertheless, in part due to technical limitations, the mechanisms governing this stability are not fully understood. Here, using a strategy that allows for ChIP-seq combined with RNA-seq in sparse neuronal populations in vivo, we present, to our knowledge, the first comparative analysis of permissive and repressive histone modifications in adult midbrain dopaminergic neurons, raphe nuclei serotonergic neurons and embryonic neural progenitors. Our results support a model wherein a sequential deposition of the repressive modifications H3K27me3 and H3K9me3 occur on developmental genes in a neuronal subtype specific manner. We furthermore show that aberrant gene expression during dopaminergic stress in a mouse model of Parkinson’s disease, or after methamphetamine injection, is characterized by the de-repression of genes with promoter regions that are dually marked by H3K4me3 and H3K27me3, whereas the induction of genes with promoter regions marked by any other combination of H3K27me3 and H3K9me3 occur less frequently. Our study provides to our knowledge the first genome-wide analysis of permissive/repressive histone modifications coupled to gene expression in these rare but clinically relevant neuronal subtypes. This strategy can be generalized for the identification and functional characterization of molecular determinants involved in the maintenance of gene expression in other classes of neurons. Overall design: 16 samples in total from 8 mice. 8 TRAP-seq samples: 4 from methamphetamine treated mice, 4 from saline treated mice. 8 RNA-seq samples performed on total RNA from the unbound fraction of each TRAP sample."],"repository":["ENA"],"description_synonyms":["Regulations, Materials, Meth, methionine aminopeptidase activity, adult stage, Gene, sryalpha, Sialic acid-binding Ig-like lectin 1, Chalk, cobalamin-dependent methionine synthase activity, Social Controls, std, Histone H2b, Histone H2a, srybeta, 5-methyltetrahydrofolate:L-homocysteine S-methyltransferase activity, MetH, mel(3)8, Tina, smooth ER, 2, sry-beta, Serotoninergic Neuron, 5-methyltetrahydrofolate--homocysteine transmethylase activity, Serotonergic, Formal Social Controls, familial adenomatous polyposis, adult, methionine synthase (cobalamin-dependent) activity, N(5)-methyltetrahydrofolate methyltransferase activity, MAP, peptidase M activity, Histone H3.3, adenomas, SER, sry alpha, rabGAPLP, tetrahydrofolate methyltransferase activity, B12 N5-methyltetrahydrofolate homocysteine methyltransferase activity, L-methionine aminopeptidase activity, N5-methyltetrahydrofolic-homocysteine vitamin B12 transmethylase activity, DmelCG6127, Glass, Genetic, Sryalpha, Siglec-1, familial adenomatous polyposis 2, sry beta, RabGAP-5, SN, autosomal recessive multiple colorectal adenomas, Social, ser, Bd, N(5)-methyltetrahydrofolate--homocysteine cobalamin methyltransferase activity, Neurons, Ice, RUSC3, Sa, N5-methyltetrahydrofolate-homocysteine cobalamin methyltransferase activity, Histone H5, Histone H4, Histone H7, Neuron, tetrahydropteroylglutamate methyltransferase activity, Histone H1, CG7938, CD169, Histone H3, MUTYH-Associated Polyposis, Formal Social Control, MYH-associated polyposis, srya, autosomal recessive familial adenomatous polyposis, Maps, Cistrons, Histone, sryb, B12 N(5)-methyltetrahydrofolate homocysteine methyltransferase activity, Crystal., Social Control, Genetic Materials, N-methyltetrahydrofolate:L-homocysteine methyltransferase activity, Adults, Genetic Material, autosomal recessive, RUTBC3, sry-a, tetrahydropteroylglutamic methyltransferase activity, sry-b, Srybeta, DmelCG7938, Serotoninergic, Control, 5-methyltetrahydrofolate-homocysteine S-methyltransferase activity, N5-methyltetrahydrofolate methyltransferase activity, INSDC_feature:gene, Serotoninergic Neurons, Serotonergic Neuron, Rpw, MYH-Associated Polyposis, Controls, Sheep erythrocyte receptor, Histone H1(s), N(5)-methyltetrahydrofolic--homocysteine vitamin B12 transmethylase activity, RABGAP5, Speed, sry-alpha, CG17957, CT18858, Material, multiple colorectal, vitamin B12 methyltransferase activity, CG6127, methyltetrahydrofolate--homocysteine vitamin B12 methyltransferase activity, MAP syndrome, Cistron, regulation, Sry alpha, DmelCG17957, Regulation, sry, FAP2, 5-methyltetrahydrofolate--homocysteine S-methyltransferase activity, colorectal adenomatous polyposis"],"name_synonyms":["Regulations, Materials, Meth, methionine aminopeptidase activity, adult stage, Gene, sryalpha, Sialic acid-binding Ig-like lectin 1, Chalk, cobalamin-dependent methionine synthase activity, Social Controls, std, Histone H2b, Histone H2a, srybeta, 5-methyltetrahydrofolate:L-homocysteine S-methyltransferase activity, MetH, mel(3)8, Tina, smooth ER, 2, sry-beta, Serotoninergic Neuron, 5-methyltetrahydrofolate--homocysteine transmethylase activity, Serotonergic, Formal Social Controls, familial adenomatous polyposis, adult, methionine synthase (cobalamin-dependent) activity, N(5)-methyltetrahydrofolate methyltransferase activity, MAP, peptidase M activity, Histone H3.3, adenomas, SER, sry alpha, rabGAPLP, tetrahydrofolate methyltransferase activity, B12 N5-methyltetrahydrofolate homocysteine methyltransferase activity, L-methionine aminopeptidase activity, N5-methyltetrahydrofolic-homocysteine vitamin B12 transmethylase activity, DmelCG6127, Glass, Genetic, Sryalpha, Siglec-1, familial adenomatous polyposis 2, sry beta, RabGAP-5, SN, autosomal recessive multiple colorectal adenomas, Social, ser, Bd, N(5)-methyltetrahydrofolate--homocysteine cobalamin methyltransferase activity, Neurons, Ice, RUSC3, Sa, N5-methyltetrahydrofolate-homocysteine cobalamin methyltransferase activity, Histone H5, Histone H4, Histone H7, Neuron, tetrahydropteroylglutamate methyltransferase activity, Histone H1, CG7938, CD169, Histone H3, MUTYH-Associated Polyposis, Formal Social Control, MYH-associated polyposis, srya, autosomal recessive familial adenomatous polyposis, Maps, Cistrons, Histone, sryb, B12 N(5)-methyltetrahydrofolate homocysteine methyltransferase activity, Crystal., Social Control, Genetic Materials, N-methyltetrahydrofolate:L-homocysteine methyltransferase activity, Adults, Genetic Material, autosomal recessive, RUTBC3, sry-a, tetrahydropteroylglutamic methyltransferase activity, sry-b, Srybeta, DmelCG7938, Serotoninergic, Control, 5-methyltetrahydrofolate-homocysteine S-methyltransferase activity, N5-methyltetrahydrofolate methyltransferase activity, INSDC_feature:gene, Serotoninergic Neurons, Serotonergic Neuron, Rpw, MYH-Associated Polyposis, Controls, Sheep erythrocyte receptor, Histone H1(s), N(5)-methyltetrahydrofolic--homocysteine vitamin B12 transmethylase activity, RABGAP5, Speed, sry-alpha, CG17957, CT18858, Material, multiple colorectal, vitamin B12 methyltransferase activity, CG6127, methyltetrahydrofolate--homocysteine vitamin B12 methyltransferase activity, MAP syndrome, Cistron, regulation, Sry alpha, DmelCG17957, Regulation, sry, FAP2, 5-methyltetrahydrofolate--homocysteine S-methyltransferase activity, colorectal adenomatous polyposis"],"additional_accession":[]},"is_claimable":false,"name":"A comprehensive map coupling histone modifications with gene regulation in adult dopaminergic and serotonergic neurons [TRAP-Seq SER_Meth]","description":"A comprehensive map coupling histone modifications with gene regulation in adult dopaminergic and serotonergic neurons [TRAP-Seq SER_Meth]","dates":{"last_updated":"2025-09-24","first_public":"2018-03-01"},"accession":"PRJNA423285","cross_references":{"GEO":["GSE108372"],"taxon":["10090"],"PubMed":["29581424"]}}