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Series GSE132403 Query DataSets for GSE132403
Status Public on Jan 23, 2020
Title Chromatin accessibility dynamics in a model of human forebrain development
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary In this study, we used a forebrain 3D spheroid model to map chromatin accessibility and gene expression changes throughout a dense time course spanning 20 months of neuronal and glial maturation.
 
Overall design We generated more than 100 ATAC-seq libraries from iPSC to 20 months in culture.

>>>Submitter states that the raw data will be made available through dbGaP due to patient privacy concerns<<<<
Web link http://brainchromatin.stanford.edu
 
Contributor(s) Trevino AE, Sinnott-Armstrong N, Andersen J, Yoon S, Huber N, Chang HY, Pritchard JK, Greenleaf WJ, Pasca SP
Citation(s) 31974223
Submission date Jun 07, 2019
Last update date Feb 04, 2020
Contact name Nasa Sinnott-Armstrong
Organization name Stanford University
Department Genetics
Lab Pritchard Lab
Street address 318 Campus Drive, Clark Center S240
City Stanford
State/province California
ZIP/Postal code 94305
Country USA
 
Platforms (1)
GPL21697 NextSeq 550 (Homo sapiens)
Samples (139)
GSM3896901 001_neuronal_371_2242.1_hSS
GSM3896902 002_neuronal_371_8858.1_hCS
GSM3896903 003_neuronal_371_8858.1_hSS
Relations
BioProject PRJNA549493

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
GSE132403_Data_01_all_peaks.tsv.gz 5.9 Mb (ftp)(http) TSV
GSE132403_Data_02_merged_peaks_updated.tsv.gz 2.7 Mb (ftp)(http) TSV
GSE132403_Data_03_all_peak_counts_updated.tsv.gz 66.5 Mb (ftp)(http) TSV
GSE132403_Data_04_merged_peak_counts_updated2.tsv.gz 38.1 Mb (ftp)(http) TSV
GSE132403_Data_05_early_spheres_vs_HFT.tsv.gz 21.5 Mb (ftp)(http) TSV
GSE132403_Data_06_d200_hCS_glia_vs_HFT.tsv.gz 18.1 Mb (ftp)(http) TSV
GSE132403_Data_07_d200_hCS_neurons_vs_HFT.tsv.gz 19.0 Mb (ftp)(http) TSV
GSE132403_Data_08_distal_variable_peaks_counts_matrix_EdgeR_QN.tsv.gz 314.7 Mb (ftp)(http) TSV
GSE132403_Data_09_distal_variable_peaks_counts_matrix_EdgeR_QN_top40pct.tsv.gz 147.8 Mb (ftp)(http) TSV
GSE132403_Data_10_KM3_Clusters_distal_working_counts_matrix_EdgeR_QN_top40pct_peaks.tsv.gz 3.2 Mb (ftp)(http) TSV
GSE132403_Data_11_early_hSS_vs_hCS.tsv.gz 19.4 Mb (ftp)(http) TSV
GSE132403_Data_12_middle_hSS_vs_hCS.tsv.gz 20.0 Mb (ftp)(http) TSV
GSE132403_Data_13_old_hSS_vs_hCS.tsv.gz 19.4 Mb (ftp)(http) TSV
GSE132403_Data_14_subpallium_peaks.tsv.gz 250.4 Kb (ftp)(http) TSV
GSE132403_Data_15_Batch_corrected_rna_counts_matrix.tsv.gz 14.0 Mb (ftp)(http) TSV
GSE132403_Data_16_ATAC_RNA_correlations_binned_500k.tsv.gz 82.2 Mb (ftp)(http) TSV
GSE132403_Data_17_LD_Score_regression_cluster_enrichments.txt.gz 7.4 Kb (ftp)(http) TXT
GSE132403_Data_18_Motif_presence_distal_variable_peaks_EdgeR_QN_top40pct.tsv.gz 10.8 Mb (ftp)(http) TSV
GSE132403_Data_19_chromVAR_deviations.tsv.gz 401.2 Kb (ftp)(http) TSV
GSE132403_Data_20_chromVAR_variabilities.tsv.gz 13.2 Kb (ftp)(http) TSV
GSE132403_Data_21_TF_RNA_correlations.tsv.gz 2.2 Mb (ftp)(http) TSV
GSE132403_Data_22_early_hCS_neuronal_vs_others.tsv.gz 102.2 Mb (ftp)(http) TSV
GSE132403_RAW.tar 480.7 Mb (http)(custom) TAR (of NARROWPEAK)
Raw data not provided for this record
Processed data provided as supplementary file
Processed data are available on Series record
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