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Series GSE129017 Query DataSets for GSE129017
Status Public on May 05, 2020
Title Allele-specific open chromatin in human neurons elucidates functional noncoding disease variants
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary ASoC variants are prevalent and cell type-specific ASoC variants were over-represented in intergenic regions and active enhancers. The collection includes ATAC-Seq and RNA-Seq data that were taken from human iPS cells and their derived neuronal cells (neural progenitor cells, cortical glutamatergic neurons, GABAergic neurons, and dopaminergic neurons).
Overall design In order to detect the changes in chromatin accessibility as well as associated changes at the transcriptional level during neuronal differentiation, we applied human induced pluripotent stem cells (hiPSCs) and hiPSC-derived neurons as a neurodevelopmental model. Generally, 8 iPSC lines from RUCDR were induced to differentiate into neural progenitor cells (NPC), 15-day cortical glutamatergic neurons (CN, Glut d15), GABAergic neurons, and dopaminergic neurons. Their open chromatin landscape, as well as transcriptional activities, were measured using ATAC-Seq and bulk RNA-Seq, respectively. An additional 12 lines were used to generate NPC cells and Glut-d15 neurons for ATAC-Seq, with the aim in gaining extended statistic power for ASoC analysis.
Contributor(s) Duan J, Zhang S
Citation(s) 32732423, 34308291
NIH grant(s)
Grant ID Grant title Affiliation Name
R01 MH106575 Systematic Functional Interpretation of Regulatory Variants in Schizophrenia NorthShore University HealthSystem Jubao Duan
Submission date Mar 28, 2019
Last update date Jul 28, 2021
Contact name Jubao Duan
Phone (224) 364-7564
Organization name NorthShore University HealthSystem
Department Center for Psychiatric Genetics
Lab Unit of Functional Genomics in Psychiatry
Street address 1001 University Place
City Evanston
State/province IL
ZIP/Postal code 60201
Country USA
Platforms (2)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Samples (118)
GSM3690689 CN_02_ATAC_Seq
GSM3690690 CN_03_ATAC_Seq
GSM3690691 CN_04_ATAC_Seq
BioProject PRJNA529717
SRA SRP189815

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Supplementary file Size Download File type/resource
GSE129017_RNASeq_JDuan_raw_reads.txt.gz 6.7 Mb (ftp)(http) TXT
GSE129017_cleanup_CN_max.bed.gz 3.2 Mb (ftp)(http) BED
GSE129017_cleanup_DN_max.bed.gz 3.6 Mb (ftp)(http) BED
GSE129017_cleanup_GA_max.bed.gz 3.7 Mb (ftp)(http) BED
GSE129017_cleanup_NPC_max.bed.gz 3.2 Mb (ftp)(http) BED
GSE129017_cleanup_all_5_cell_types_peaks.bed.gz 8.5 Mb (ftp)(http) BED
GSE129017_cleanup_ips_max.bed.gz 4.4 Mb (ftp)(http) BED
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