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Status |
Public on Jun 04, 2021 |
Title |
HyDrop: droplet-based scATAC-seq and scRNA-seq using dissolvable hydrogel beads |
Organisms |
Drosophila melanogaster; Homo sapiens; Mus musculus |
Experiment type |
Genome binding/occupancy profiling by high throughput sequencing Expression profiling by high throughput sequencing
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Summary |
We developed HyDrop, a new droplet microfluidic single-cell sequencing protocol for single-cell ATAC-seq and single-cell RNA-seq. We applied HyDrop-ATAC to flash-frozen mouse cortex and generated 7996 single-cell chromatin accessibility profiles. We applied HyDrop-RNA to flash-frozen mouse cortex and generated 9508 single-cell transcriptomes. We also applied HyDrop-RNA to a small population of FAC-sorted neurons from the Drosophila brain to demonstrate the protocol's applicability to low-input samples. The data available in this repository can be used to replicate all the figures in our manuscript using our data analysis tutorial available here: https://github.com/aertslab/hydrop_data_analysis
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Overall design |
HyDrop-ATAC on mixed species cell lines and mouse cortex nuclei. HyDrop-RNA on mixed-species cell lines, mouse cortex nuclei and FAC-sorted drosophila neurons.
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Contributor(s) |
De Rop F, Ismail J, Bravo González-Blas C, Hulselmans G, Flerin C, Janssens J, Christiaens V, Poovathingal S, Aerts S |
Citation(s) |
35195064 |
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Submission date |
May 27, 2021 |
Last update date |
Apr 19, 2022 |
Contact name |
Stein Aerts |
E-mail(s) |
stein.aerts@kuleuven.be
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Organization name |
KU Leuven
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Lab |
Lab of Computational Biology
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Street address |
O&N4 Herestraat 49 PO Box 602
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City |
Leuven |
State/province |
Vlaams-Brabant |
ZIP/Postal code |
3000 |
Country |
Belgium |
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Platforms (4)
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GPL19969 |
Illumina MiSeq (Homo sapiens; Mus musculus) |
GPL30172 |
NextSeq 2000 (Mus musculus) |
GPL30202 |
NextSeq 2000 (Homo sapiens; Mus musculus) |
GPL30203 |
NextSeq 2000 (Drosophila melanogaster) |
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Samples (20)
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GSM5343842 |
HYA__7d0f30__20210305_barnyard_MCF-7_MMel_1-1_S1 |
GSM5343843 |
HYA__932b0e__20210309_mouse_cortex_MCF-7_PC3_1-1_S2 |
GSM5343844 |
HYA__af8d60__20210309_mouse_cortex_MCF-7_PC3_1-2_S3 |
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Relations |
BioProject |
PRJNA733185 |
SRA |
SRP321653 |