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Series GSE100033 Query DataSets for GSE100033
Status Public on Jan 27, 2018
Title Single-nucleus analysis of accessible chromatin in developing mouse forebrain reveals cell-type-specific transcriptional regulation
Organisms Homo sapiens; Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Expression profiling by high throughput sequencing
Summary Analysis of chromatin accessibility can reveal transcriptional regulatory sequences, but heterogeneity of primary tissues poses a significant challenge in mapping the precise chromatin landscape in specific cell types. Here we report single-nucleus ATAC-seq, a combinatorial barcoding-assisted single-cell assay for transposase-accessible chromatin that is optimized for use on flash-frozen primary tissue samples. We apply this technique on the mouse forebrain through eight developmental stages. Through analysis of more than 15,000 nuclei, we identify 20 distinct cell populations corresponding to major neuronal and non-neuronal cell types. We further define cell-type-specific transcriptional regulatory sequences, infer potential master transcriptional regulators and delineate developmental changes in forebrain cellular composition. Our results provide insight into the molecular and cellular dynamics that underlie forebrain development in the mouse and establish technical and analytical frameworks that are broadly applicable to other heterogeneous tissues.
Overall design We performed combinatorial single-nucleus ATAC-seq for 7 stages of embryonic forebrain development from E11.5 to P0 and adult forebrain. Data analysis pipeline used in this study:
Citation(s) 29434377, 29497140
Submission date Jun 14, 2017
Last update date Jul 25, 2021
Contact name Rongxin Fang
Organization name Ludwig Institute for Cancer Research
Lab Ren Lab
Street address 9500 Gilman Dr #3080
City La Jolla
State/province CA
ZIP/Postal code 92093
Country USA
Platforms (3)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
GPL21103 Illumina HiSeq 4000 (Mus musculus)
GPL22245 Illumina HiSeq 2500 (Homo sapiens; Mus musculus)
Samples (11)
GSM2668117 E11.5_Forebrain_scATAC_Rep1_Rep2
GSM2668118 E12.5_Forebrain_scATAC_Rep1_Rep2
GSM2668119 E13.5_Forebrain_scATAC_Rep1_Rep2
BioProject PRJNA390526
SRA SRP133390

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Supplementary file Size Download File type/resource
GSE100033_RAW.tar 305.8 Mb (http)(custom) TAR (of BW, MAT, TXT)
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Raw data are available in SRA

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