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Series GSE162798 Query DataSets for GSE162798
Status Public on Oct 20, 2021
Title Simple oligonucleotide-based multiplexing of single-cell chromatin accessibility
Organisms Homo sapiens; Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Expression profiling by high throughput sequencing
Summary we reported the development of an accurate, easy-to-use and scalable system (SNuBar) for multiplexing single cell ATAC or multi-omics (ATAC&RNA) assays, and applied this method to multiplex therapy combinations in a lung cancer mouse model and macro-spatial regions of normal breast tissues and samples.
Overall design SNuBar multiplexes scATAC-seq and scATAC&RNA-seq with unmodified oligonucleotides, identfies treatment-induced chromatin dynamics in 28 mice with lung tumors, profiles epigenetic heterogeneity of 32 spatial regions in normal breast tissues, identifies TFs that regulated breast cell type identities.
Contributor(s) Wang K, Xiao Z, Yan Y, Navin N
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Submission date Dec 07, 2020
Last update date Oct 22, 2021
Contact name Anil K Sood
Organization name MDACC
Department genetics
Lab Navin Lab
Street address 6767 Bertner Ave
City Houston
State/province TX
ZIP/Postal code 77030
Country USA
Platforms (6)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
GPL16512 Illumina HiSeq 2000 (Homo sapiens; Mus musculus)
Samples (15)
GSM4960033 SnubarHighAK
GSM4960034 SnubarLowAK
GSM4960035 Snubar-96plex
BioProject PRJNA683040
SRA SRP296812

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
GSE162798_RAW.tar 24.9 Gb (http)(custom) TAR (of BED, CSV, MTX, TBI, TSV)
GSE162798_readme_BCfastqs_SRRs.txt 1.2 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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