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Series GSE152423 Query DataSets for GSE152423
Status Public on Sep 23, 2021
Title Multi-modal characterization of chromatin architecture from 24 hpf whole zebrafish embryos
Organism Danio rerio
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Other
Summary DNA accessibility of cis regulatory elements (CREs) dictates transcriptional activity and drives cell differentiation during development. To obtain a more comprehensive view of CRE dynamics, we applied single-cell combinatorial indexing ATAC-seq (sci-ATAC-seq) to whole 24hpf stage zebrafish embryos thereby measuring DNA accessibility in ~23,000 single cells. We developed two solutions to computational challenges in analyzing single-cell accessibility maps: 1) selection of informative genome segments, and 2) genome-wide classification of both cell-type-specific and multi-cell-type accessibility dynamics. We validated the sci-ATAC-seq results with bulk measurements for histone post-translational modifications and 3D genome organization, recovering known relationships between chromatin modalities and providing additional regulatory classifications. Furthermore, we applied sci-ATAC-seq to cloche/npas4l mutant embryos which revealed known and novel cellular roles for the hemato-vascular transcriptional master regulator, and suggested an intricate network regulating its expression. These data and their extensive analysis constitute a valuable developmental, molecular, and computational resource for future studies.
 
Overall design ChIP-seq for 5 histone post-translational modifications with two replicates each and input controls; in situ Hi-C sequenced across three lanes; two replicates of chromatin-associated RNA-seq; and single-cell combinatorial indexing ATAC-seq performed twice on wild-type embryos and once on mixed embryos wild-type, heterozygous, and homozygous npas4lbns297
 
Contributor(s) Lacadie SA, Ohler U
Citation(s) 36777038
Submission date Jun 13, 2020
Last update date Mar 02, 2023
Contact name Scott Allen Lacadie
E-mail(s) scott.lacadie@mdc-berlin.de
Organization name Max Delbrück Center for Molecular Medicine
Department Berlin Institute for Medical Systems Biology
Lab Ohler
Street address Robert-Rössle-Str. 10
City Berlin-Buch
ZIP/Postal code 13092
Country Germany
 
Platforms (2)
GPL20828 Illumina NextSeq 500 (Danio rerio)
GPL21741 Illumina HiSeq 4000 (Danio rerio)
Samples (21)
GSM4615118 ChIP-seq input for H3K4me1, H3K4me2, H3K4me3, and H3K27ac replicate 1
GSM4615119 ChIP-seq input for H3K4me1, H3K4me2, H3K4me3, and H3K27ac replicate 2
GSM4615120 H3K4me1 ChIP-seq replicate 1
Relations
BioProject PRJNA639281
SRA SRP267183

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
GSE152423_SupplTab6_scregseg-pi_segmentation.tsv.gz 817.6 Mb (ftp)(http) TSV
GSE152423_cells.tsv.gz 137.7 Kb (ftp)(http) TSV
GSE152423_chromRNA_fwd.bw 247.2 Mb (ftp)(http) BW
GSE152423_chromRNA_rev.bw 259.4 Mb (ftp)(http) BW
GSE152423_clusterPseudoBulkCountMatrix.mtx.gz 119.0 Mb (ftp)(http) MTX
GSE152423_h3k27ac.bw 189.6 Mb (ftp)(http) BW
GSE152423_h3k27ac.narrowPeak.gz 5.6 Mb (ftp)(http) NARROWPEAK
GSE152423_h3k36me3.bw 189.0 Mb (ftp)(http) BW
GSE152423_h3k4me1.bw 189.6 Mb (ftp)(http) BW
GSE152423_h3k4me1.narrowPeak.gz 8.2 Mb (ftp)(http) NARROWPEAK
GSE152423_h3k4me2.bw 188.9 Mb (ftp)(http) BW
GSE152423_h3k4me2.narrowPeak.gz 4.8 Mb (ftp)(http) NARROWPEAK
GSE152423_h3k4me3.bw 189.5 Mb (ftp)(http) BW
GSE152423_h3k4me3.narrowPeak.gz 6.3 Mb (ftp)(http) NARROWPEAK
GSE152423_scregeseg_fi_regions.bed.gz 769.7 Kb (ftp)(http) BED
GSE152423_singleCellCountMatrix.mtx.gz 134.8 Mb (ftp)(http) MTX
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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