NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Series GSE136656 Query DataSets for GSE136656
Status Public on Nov 27, 2020
Title Activity-dependent regulome and transcriptome of human GABAergic neurons reveal new patterns of gene regulation and neurological disease heritability
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary Neuronal activity-dependent gene expression is essential for healthy brain development. Emerging studies implicate alterations in GABAergic neuronal circuits in neurodevelopmental and psychiatric disorders. We conducted an activity-dependent transcriptional and epigenetic profiling of human iPSC-derived GABAergic neurons.
 
Overall design iCell GABAneurons were characterized by total and single-cell RNA sequencing and found to have similar transcriptional profiles to developing subcortical GABAergic neurons. These cultures were grown for 14-16 days in vitro prior to silencing with 2-amino-5-phosphonopentanoic acid and tetrodotoxin for 12 hours, followed by stimulation with 55mM potassium chloride for various time points prior to harvesting cells for RNA sequencing, ATAC sequencing or ChIP sequencing.
 
Contributor(s) Boulting GL, Duressi E, Ataman B, Harmin DA, Mei K, Carter A, Greenberg ME
Citation(s) 33542524
Submission date Aug 29, 2019
Last update date Feb 10, 2021
Contact name Gabriella Lutz Boulting
Organization name Harvard Medical School
Department Neurobiology
Lab Greenberg Lab
Street address 200 Longwood Ave.
City Boston
State/province MA
ZIP/Postal code 02115
Country USA
 
Platforms (1)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
Samples (130)
GSM4054634 iCell_ATAC_KCl-0hr_B1_1
GSM4054635 iCell_ATAC_KCl-0hr_B2_1
GSM4054636 iCell_ATAC_KCl-0hr_B3_1
Relations
BioProject PRJNA563023
SRA SRP219925

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE136656_1711_Indrops_v2_and_v3.jpg.gz 544.9 Kb (ftp)(http) JPG
GSE136656_1CellBio_barcode_v2.txt.gz 1.2 Mb (ftp)(http) TXT
GSE136656_Boulting_2019_SuppData2_scRNAseq_Seurat.Rda.gz 1.2 Gb (ftp)(http) RDA
GSE136656_RAW.tar 1.1 Gb (http)(custom) TAR (of TSV, TXT)
GSE136656_human_f-CTX_ChIP.bw.tar.gz 2.4 Gb (ftp)(http) TAR
GSE136656_iCell_4G_Total_GRCh38.p2_KCl-15m-vs-0hr_4-vs-4-reps_DifflExpr.tsv.gz 2.0 Mb (ftp)(http) TSV
GSE136656_iCell_4G_Total_GRCh38.p2_KCl-1hr-vs-0hr_3-vs-4-reps_DifflExpr.tsv.gz 2.0 Mb (ftp)(http) TSV
GSE136656_iCell_4G_Total_GRCh38.p2_KCl-2hr-vs-0hr_4-vs-4-reps_DifflExpr.tsv.gz 2.1 Mb (ftp)(http) TSV
GSE136656_iCell_4G_Total_GRCh38.p2_KCl-4hr-vs-0hr_4-vs-4-reps_DifflExpr.tsv.gz 2.1 Mb (ftp)(http) TSV
GSE136656_iCell_ATAC.bw.tar.gz 2.8 Gb (ftp)(http) TAR
GSE136656_iCell_ChIP.bw.tar.gz 6.4 Gb (ftp)(http) TAR
GSE136656_iCell_Single-cell_counts.tsv.tar.gz 177.8 Mb (ftp)(http) TAR
GSE136656_iCell_Total_GRCh37.p5_KCl-15m-vs-0hr_3-vs-6-reps_DifflExpr.tsv.gz 2.0 Mb (ftp)(http) TSV
GSE136656_iCell_Total_GRCh37.p5_KCl-1hr-vs-0hr_3-vs-6-reps_DifflExpr.tsv.gz 2.0 Mb (ftp)(http) TSV
GSE136656_iCell_Total_GRCh37.p5_KCl-2hr-vs-0hr_6-vs-6-reps_DifflExpr.tsv.gz 2.2 Mb (ftp)(http) TSV
GSE136656_iCell_Total_GRCh37.p5_KCl-4hr-vs-0hr_3-vs-6-reps_DifflExpr.tsv.gz 2.1 Mb (ftp)(http) TSV
GSE136656_iCell_Total_GRCh38.p2_KCl-15m-vs-0hr_3-vs-6-reps_DifflExpr.tsv.gz 2.1 Mb (ftp)(http) TSV
GSE136656_iCell_Total_GRCh38.p2_KCl-1hr-vs-0hr_3-vs-6-reps_DifflExpr.tsv.gz 2.1 Mb (ftp)(http) TSV
GSE136656_iCell_Total_GRCh38.p2_KCl-2hr-vs-0hr_6-vs-6-reps_DifflExpr.tsv.gz 2.3 Mb (ftp)(http) TSV
GSE136656_iCell_Total_GRCh38.p2_KCl-4hr-vs-0hr_3-vs-6-reps_DifflExpr.tsv.gz 2.2 Mb (ftp)(http) TSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record
Processed data provided as supplementary file
| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap