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Series GSE190130 Query DataSets for GSE190130
Status Public on Aug 04, 2022
Title sci-ATAC-seq data
Organism Drosophila melanogaster
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Drosophila melanogaster is a powerful, long-standing model for metazoan development and gene regulation. We profiled chromatin accessibility in almost one million, and gene expression in half a million, nuclei from eleven tightly staged, overlapping windows of its embryogenesis. Leveraging the asynchronicity of embryos within each collection, we developed a statistical model to more precisely estimate the age of each nucleus, resulting in continuous views of molecular and cellular transitions throughout the majority of embryonic development. From these data, we identify cell types, infer their developmental relationships, and link cell type-specific changes to dynamic changes in enhancer usage, transcription factor (TF) expression and the accessibility of TFs’ cognate motifs. Looking forward, this strategy may facilitate future investigations of gene regulation in vivo at arbitrarily high temporal resolution.
Overall design Staged Drosophila embryos were collected in 11 overlapping time windows, collectively spanning 0-20 hrs of development at 25°C. Overlapping two-hour collections were used to capture the rapid transitions during early embryogenesis, followed by overlapping four-hour collections from 4-6 hrs onwards (Fig. 1A). From each such collection, embryo collections were halved and separately processed for single cell ATAC-seq or single cell RNA-seq.
Contributor(s) Calderon D, Blecher-Gonen R, Huang X
Citation(s) 35926038
Submission date Dec 03, 2021
Last update date Aug 15, 2022
Contact name Diego Calderon
Organization name University of Washington
Street address 3720 15th Ave NE
City Seattle
ZIP/Postal code 98105
Country USA
Platforms (1)
GPL25244 Illumina NovaSeq 6000 (Drosophila melanogaster)
Samples (108)
GSM5714979 exp1_r1_GM+CH12.barnyard_b1_L001
GSM5714980 exp1_r1_GM+CH12.barnyard_b1_L002
GSM5714981 exp1_r1_GM+CH12.barnyard_b1_L003
This SubSeries is part of SuperSeries:
GSE190149 The continuum of Drosophila embryonic development at single cell resolution
BioProject PRJNA785974
SRA SRP349166

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
GSE190130_exp1_hrs03-07_b1.peak_matrix.columns.txt.gz 1.2 Mb (ftp)(http) TXT
GSE190130_exp1_hrs03-07_b1.peak_matrix.mtx.gz 1.7 Gb (ftp)(http) MTX
GSE190130_exp1_hrs03-07_b1.peak_matrix.rows.txt.gz 795.6 Kb (ftp)(http) TXT
GSE190130_exp1_hrs04-08_b1.peak_matrix.columns.txt.gz 1.0 Mb (ftp)(http) TXT
GSE190130_exp1_hrs04-08_b1.peak_matrix.mtx.gz 1.5 Gb (ftp)(http) MTX
GSE190130_exp1_hrs04-08_b1.peak_matrix.rows.txt.gz 795.6 Kb (ftp)(http) TXT
GSE190130_exp1_hrs06-10_b1.peak_matrix.columns.txt.gz 956.3 Kb (ftp)(http) TXT
GSE190130_exp1_hrs06-10_b1.peak_matrix.mtx.gz 2.0 Gb (ftp)(http) MTX
GSE190130_exp1_hrs06-10_b1.peak_matrix.rows.txt.gz 795.6 Kb (ftp)(http) TXT
GSE190130_exp1_hrs08-12_b1.peak_matrix.columns.txt.gz 1.4 Mb (ftp)(http) TXT
GSE190130_exp1_hrs08-12_b1.peak_matrix.mtx.gz 2.1 Gb (ftp)(http) MTX
GSE190130_exp1_hrs08-12_b1.peak_matrix.rows.txt.gz 795.6 Kb (ftp)(http) TXT
GSE190130_exp1_hrs10-14_b1.peak_matrix.columns.txt.gz 630.4 Kb (ftp)(http) TXT
GSE190130_exp1_hrs10-14_b1.peak_matrix.mtx.gz 1.0 Gb (ftp)(http) MTX
GSE190130_exp1_hrs10-14_b1.peak_matrix.rows.txt.gz 795.6 Kb (ftp)(http) TXT
GSE190130_exp1_hrs12-16_b1.peak_matrix.columns.txt.gz 553.8 Kb (ftp)(http) TXT
GSE190130_exp1_hrs12-16_b1.peak_matrix.mtx.gz 1.1 Gb (ftp)(http) MTX
GSE190130_exp1_hrs12-16_b1.peak_matrix.rows.txt.gz 795.6 Kb (ftp)(http) TXT
GSE190130_exp1_hrs14-18_b1.peak_matrix.columns.txt.gz 352.3 Kb (ftp)(http) TXT
GSE190130_exp1_hrs14-18_b1.peak_matrix.mtx.gz 628.2 Mb (ftp)(http) MTX
GSE190130_exp1_hrs14-18_b1.peak_matrix.rows.txt.gz 795.6 Kb (ftp)(http) TXT
GSE190130_exp1_hrs16-20_b1.peak_matrix.columns.txt.gz 666.6 Kb (ftp)(http) TXT
GSE190130_exp1_hrs16-20_b1.peak_matrix.mtx.gz 975.2 Mb (ftp)(http) MTX
GSE190130_exp1_hrs16-20_b1.peak_matrix.rows.txt.gz 795.6 Kb (ftp)(http) TXT
GSE190130_exp2_hrs00-02_b2.peak_matrix.columns.txt.gz 484.0 Kb (ftp)(http) TXT
GSE190130_exp2_hrs00-02_b2.peak_matrix.mtx.gz 119.2 Mb (ftp)(http) MTX
GSE190130_exp2_hrs00-02_b2.peak_matrix.rows.txt.gz 795.6 Kb (ftp)(http) TXT
GSE190130_exp2_hrs01-03_b2.peak_matrix.columns.txt.gz 189.3 Kb (ftp)(http) TXT
GSE190130_exp2_hrs01-03_b2.peak_matrix.mtx.gz 254.8 Mb (ftp)(http) MTX
GSE190130_exp2_hrs01-03_b2.peak_matrix.rows.txt.gz 795.6 Kb (ftp)(http) TXT
GSE190130_exp2_hrs02-04_b2.peak_matrix.columns.txt.gz 502.1 Kb (ftp)(http) TXT
GSE190130_exp2_hrs02-04_b2.peak_matrix.mtx.gz 635.5 Mb (ftp)(http) MTX
GSE190130_exp2_hrs02-04_b2.peak_matrix.rows.txt.gz 795.6 Kb (ftp)(http) TXT
GSE190130_exp2_hrs03-07_b2.peak_matrix.columns.txt.gz 293.8 Kb (ftp)(http) TXT
GSE190130_exp2_hrs03-07_b2.peak_matrix.mtx.gz 514.4 Mb (ftp)(http) MTX
GSE190130_exp2_hrs03-07_b2.peak_matrix.rows.txt.gz 795.6 Kb (ftp)(http) TXT
GSE190130_exp2_hrs10-14_b1.peak_matrix.columns.txt.gz 195.8 Kb (ftp)(http) TXT
GSE190130_exp2_hrs10-14_b1.peak_matrix.mtx.gz 414.1 Mb (ftp)(http) MTX
GSE190130_exp2_hrs10-14_b1.peak_matrix.rows.txt.gz 795.6 Kb (ftp)(http) TXT
GSE190130_exp2_hrs12-16_b1.peak_matrix.columns.txt.gz 81.4 Kb (ftp)(http) TXT
GSE190130_exp2_hrs12-16_b1.peak_matrix.mtx.gz 306.7 Mb (ftp)(http) MTX
GSE190130_exp2_hrs12-16_b1.peak_matrix.rows.txt.gz 795.6 Kb (ftp)(http) TXT
GSE190130_exp2_hrs14-18_b1.peak_matrix.columns.txt.gz 163.4 Kb (ftp)(http) TXT
GSE190130_exp2_hrs14-18_b1.peak_matrix.mtx.gz 340.1 Mb (ftp)(http) MTX
GSE190130_exp2_hrs14-18_b1.peak_matrix.rows.txt.gz 795.6 Kb (ftp)(http) TXT
GSE190130_exp2_hrs16-20_b1.peak_matrix.columns.txt.gz 106.1 Kb (ftp)(http) TXT
GSE190130_exp2_hrs16-20_b1.peak_matrix.mtx.gz 294.4 Mb (ftp)(http) MTX
GSE190130_exp2_hrs16-20_b1.peak_matrix.rows.txt.gz 795.6 Kb (ftp)(http) TXT
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