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Series GSE175684 Query DataSets for GSE175684
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
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
 
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.
 
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
Submission date May 27, 2021
Last update date Apr 19, 2022
Contact name Stein Aerts
E-mail(s) stein.aerts@kuleuven.be
Organization name KU Leuven
Lab Lab of Computational Biology
Street address O&N4 Herestraat 49 PO Box 602
City Leuven
State/province Vlaams-Brabant
ZIP/Postal code 3000
Country Belgium
 
Platforms (4)
GPL19969 Illumina MiSeq (Homo sapiens; Mus musculus)
GPL30172 NextSeq 2000 (Mus musculus)
GPL30202 NextSeq 2000 (Homo sapiens; Mus musculus)
Samples (20)
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
Relations
BioProject PRJNA733185
SRA SRP321653

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
GSE175684_HYA_932b0e_af8d60_MCF-7.bwa.out.possorted.GRCH38ONLY.RPGCnormalized.bw 182.7 Mb (ftp)(http) BW
GSE175684_HYA_932b0e_af8d60_PC-3.bwa.out.possorted.GRCH38ONLY.RPGCnormalized.bw 433.5 Mb (ftp)(http) BW
GSE175684_HYA_combined_20210323_cortex_phu_dv_etssb.cluster_bigwigs.tar.gz 797.4 Mb (ftp)(http) TAR
GSE175684_HYA_combined_20210323_cortex_phu_dv_etssb.cluster_dars.tar.gz 8.5 Mb (ftp)(http) TAR
GSE175684_RAW.tar 3.8 Gb (http)(custom) TAR (of TAR, TSV)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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