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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.
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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
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Contributor(s) |
Lacadie SA, Ohler U |
Citation(s) |
36777038 |
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Submission date |
Jun 13, 2020 |
Last update date |
Mar 02, 2023 |
Contact name |
Scott Allen Lacadie |
E-mail(s) |
scott.lacadie@mdc-berlin.de
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Organization name |
Max Delbrück Center for Molecular Medicine
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Department |
Berlin Institute for Medical Systems Biology
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Lab |
Ohler
|
Street address |
Robert-Rössle-Str. 10
|
City |
Berlin-Buch |
ZIP/Postal code |
13092 |
Country |
Germany |
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Platforms (2) |
GPL20828 |
Illumina NextSeq 500 (Danio rerio) |
GPL21741 |
Illumina HiSeq 4000 (Danio rerio) |
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Samples (21)
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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 |
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 Selector |
Raw data are available in SRA |
Processed data are available on Series record |